Dissertations / Theses on the topic 'Solvation Dynamics - Biological Water'

Metal ions solvated in aqueous, non-aqueous, and mixtures of solvents occur in many chemical contexts, for example in electrochemical applications and solvent separation. Solvated ions appear in high concentration in the living organisms, where their presence or absence can fundamentally alter the functions of life. In many of these cases, understanding the selective solvation and the dynamics of the ions is essential for the understanding of the processes involved.

Computer simulation provides a molecular level of detail of the solvation process usually not available from experiments. The quality of the interaction models employed in the theoretical description is of particular importance, since even rather small changes in the interaction can lead to substantial and qualitative differences.

This thesis describes the development of a sequence of increasingly refined analytical ion-solvent potentials from ab initio calculations for the systems Li⁺(aq), Na⁺(aq), Mg²⁺(aq), Al³⁺(aq), Li⁺(MeCN), Na⁺(MeCN), Li⁺(aq, MeCN), and Na⁺(aq, MeCN). Molecular dynamics simulations using these potentials were subsequently performed, and some key-properties computed. The reliability of the computed thermodynamical, structural and dynamical properties was scrutinized.

In this thesis, we report on our studies of water dynamics and structure in various biological environments which include: the surfaces of proteins and various oligosaccharides, the intervening space between proteins; and in the vicinity of cryoprotectant disaccharides in the liquid and ice phases. From a theoretical perspective, we propose methodology to compute diffusivity and residence times on the surface of biomolecules. In particular our proposed algorithm to compute residence times appears to be better in dealing with poor statistics associated with the number of water molecules that remain on a surfaces for extended times. The type of linkage between monomers and the anomeric configuration all play a major role in determining the structure and dynamics of water on the surface of carbohydrates.

Turfgrass water use (seasonal turfET) and crop coefficients were determined and a mathematical soil-water balance model for non-weighing drainage lysimeters, which simulates the occurrence (timing and amount) of drainage, was developed. Pairs of non-weighing drainage lysimeters were used to determine crop coefficients for turfgrass in four locations in the state of Utah: Logan Golf and Country Club, Murray Golf Course, Brigham Young University (Spanish Fork) Experiment Farm, and Sunbrook Golf Course (St. George). Daily weather data including air temperature, relative humidity, average wind travel, total solar radiation, precipitation, and average soil temperature were collected with an electronic weather station at each site. Daily precipitation was measured in three sites throughout the season: Murray, Spanish Fork, and Sunbrook. At Logan Golf and Country Club, precipitation was measured to November 10,2002. Water use (averages of two lysimeters) during the growing season varied from 684 to 732 mm for three years (2000- 2002) for the mid-April through late-October observation period at Logan Golf Course; 699 mm for May through October at Murray; 469 mm at Spanish Fork; and 896 mm for late-February through early November at Sunbrook, for 2002 growing season. Calculated seasonal Etr using the 82 Kimberly Penman equation with a 1 00-miles-per-day wind travel limit varied from 1166 to 1229 mm at Logan Golf and Country Club, 1067 mm at Murray, 839 mm at Spanish Fork, and 1574 mm at Sunbrook. Seasonal Etr calculated using the PM ASCE std Etr equation was greater than the 82 Kimberly Peru11an . Seasonal Eto calculated using the FAO#56 Eto equation was less than both the 82 Kimberly Penman and the PM ASCE std Etr equations. Calculated crop coefficients (as a ratio of measured crop water use and calculated potential evapotranspiration) based on alfalfa reference evapotranspiration with the 1982 Kimberly-Penman equation averaged 0.58 for the three years at Logan. Seasonal averages varied from 0.57 to 0.60. Seasonal crop coefficients (2002) were 0.57 for Logan, Spanish Fork, and Sunbrook, and 0.65 for Murray. Short-period crop coefficients also varied within a given season. Short-term crop coefficients derived from a time of wetting and drainage experiment averaged 0.55 at Logan, 0.56 at Murray, 0.60 at Spanish Fork, and 0.56 at Sunbrook.

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2004.
Vita.
Includes bibliographical references (p. 34-35).
Hydrogen bonding between N-methylacetamide (NMA) and different solvents (D₂O or CDCl₃) was studied by using two-dimensional infrared spectroscopy to probe the frequency fluctuations of the amide I mode of the solvated NMA. An iterative fitting approach was used to extract a correlation function from the experimental data. The correlation function for NMA/D₂O was found to be biexponential with decay constants of 1050 fs and [approximately]50 fs. These timescales are interpreted as reflecting the collective rearrangement of the solution hydrogen bonding network and oscillation of the hydrogen bond bound to the NMA molecule respectively. The correlation function for NMA/CDCl₃ was found to decay on three timescales with two decay constants of 1600 fs and [approximately]50 fs, and a long time quasi-inhomogeneous component.
by Justine M. McCracken.
S.M.

Les électrolytes de type "water-in-salt" sont composés d'un sel dissous en très grande quantité dans de l'eau, au point que celle-ci devient minoritaire. Parmi ceux-ci les mélanges employant le bis(trifluoromethane) sulfonimide de lithium (LiTFSI) en tant que sels sont très prometteurs pour des applications de stockage électrochimique de l'énergie. Cependant les propriétés des liquides et des interfaces qu'ils forment ne sont pas encore bien connues. Au cours de cette thèse, nous avons réalisé des simulations de dynamique moléculaire de water-in-salts à base de LiTFSI sur une large gamme de concentration. Sa validité est fortement conditionnée par le champ de forces utilisé pour représenter les interactions entre les atomes, c'est pourquoi dans un premier temps nous avons testé une série de champs de forces issus de la littérature. Celui permettant de reproduire au mieux des mesures de viscosité et de coefficients d'auto-diffusion a alors été retenu. Nous avons ainsi pu déterminer la variation de la coordinence des ions lithium vis-à-vis des molécules d'eau et des ions TFSI avec la concentration. Nous avons pu observer que pour les systèmes les plus concentrés, une déshydratation partielle des ions lithium a lieu, ce qui impacte fortement la viscosité du milieu. Nous avons ensuite simulé des interfaces entre ces liquides et des électrodes de carbone à différents potentiels, ce qui nous a permis de déterminer la capacité de stockage. Nous avons observé une forte dissymétrie entre les électrodes positives et négatives, qui sont attribuées à la différence de taille très marquée entre les cations et les anions
“Water-in-salt” solvents are a new class of electrolytes with very promising electrochemical properties for energy storage applications. The purpose of this work is to understand the microscopic mechanisms of these superconcentrated electrolytes at play. We use atomistic molecular dynamics to simulate systems of water in LiTFSI at various salt concentrations. On the basis of comparisons of simulated and measured dynamic properties, i.e. the viscosity, diffusion coefficient and conductivity, we systematic test and develop the force fields used for the ions. As a consequence, an optimized force field is proposed, which enables the accurate modeling of such systems. The structural properties are systematically investigated on various aspects for the salt at a superconcentrated state, which shed new light on the connections between ions and water molecules. Apart from these simulations of the bulk electrolytes, we also study the water-in-salt electrolyte at interfaces, in which the capacitive performance of this electrolyte in supercapacitors are explored. The differential capacitance displays a number of nontrivial features accompanying a series of peaks in the potential region from 0 to 3 V. The study of structural evolutions of the interfacial electrolytes shows that many structural changes occur in the layer of adsorbed liquid when the potential of the electrode is changed, which are at the origin of those observed peaks in the differential capacitance

To date, there has been little research into the role of microbial community structure in the functioning of the soil ecosystem and on the links between microbial biomass size, microbial activity and key soil processes that drive nutrient availability. The maintenance of structural and functional diversity of the soil microbial community is essential to ensure the sustainability of agricultural production systems. Soils of the same type with similar fertility that had been under long-term organic and conventional crop management in Canterbury, New Zealand, were selected to investigate relationships between microbial community composition, function and potential environmental impacts. The effects of different fertilisation strategies on soil biology and nitrogen (N) dynamics were investigated under field (farm site comparison), semi-controlled (lysimeter study) and controlled (incubation experiments) conditions by determining soil microbial biomass carbon (C) and N, enzyme activities (dehydrogenase, arginine deaminase, fluorescein diacetate hydrolysis), microbial community structure (denaturing gradient gel electrophoresis following PCR amplification of 16S and 18S rDNA fragments using selected primer sets) and N dynamics (mineralisation and leaching). The farm site comparison revealed distinct differences between the soils in microbial community structure, microbial biomass C (conventional>organic) and arginine deaminase activity (organic>conventional). In the lysimeter study, the soils were subjected to the same crop rotation (barley (Hordeum vulgare L.), maize (Zea mais L.), rape (Brassica napus L. ssp. oleifera (Moench)) plus a lupin green manure (Lupinus angustifolius L.) and two fertiliser regimes (following common organic and conventional practice). Soil biological properties, microbial community structure and mineral N leaching losses were determined over 2½ years. Differences in mineral leaching losses were not significant between treatments (total organic management: 24.2 kg N ha⁻¹; conventional management: 28.6 kg N ha⁻¹). Crop rotation and plant type had a larger influence on the microbial biomass, activity and community structure than fertilisation. Initial differences between soils decreased over time for most biological soil properties, while they persisted for the enzyme activities (e.g. dehydrogenase activity: 4.0 and 2.9 µg g⁻¹ h⁻¹ for organic and conventional management history, respectively). A lack of consistent positive links between enzyme activities and microbial biomass size indicated that similarly sized and structured microbial communities can express varying rates of activity. In two successive incubation experiments, the soils were amended with different rates of a lupin green manure (4 or 8t dry matter ha⁻¹), and different forms of N at 100 kg ha⁻¹ (urea and lupin) and incubated for 3 months. Samples were taken periodically, and in addition to soil biological properties and community structure, gross N mineralisation was determined. The form of N had a strong effect on microbial soil properties. Organic amendment resulted in a 2 to 5-fold increase in microbial biomass and enzyme activities, while microbial community structure was influenced by the addition or lack of C or N substrate. Correlation analyses suggested treatment-related differences in nutrient availability, microbial structural diversity (species richness or evenness) and physiological properties of the microbial community. The findings of this thesis showed that using green manures and crop rotations improved soil biology in both production systems, that no relationships existed between microbial structure, enzyme activities and N mineralisation, and that enzyme activities and microbial community structure are more closely associated with inherent soil and environmental factors, which makes them less useful as early indicators of changes in soil quality.

Die Assoziation kleiner Moleküle (Liganden) in hydrophobe Bindungstaschen spielt eine fundamentale Rolle in der Biomolekularerkennung und den Selbstassemblierungsprozessen der physikalischen Chemie wässriger Lösungen. Während der Einfluss des Wassers auf die freie Energie der Bindung (die Bindungsaffinität) im thermischen Gleichgewicht in den letzten Jahren auf immer stärkere Aufmerksamkeit stößt, ist die Rolle des Wassers in der Kinetik und der Bestimmung der Bindungsraten noch weitestgehend unverstanden. Welche nanoskaligen Effekte des Wassers beeinflussen die Dynamik des Liganden in der Nähe der Bindungstasche, und wie lassen sie sich durch die chemischen Eigenschaften der Tasche steuern? Neuste Forschungen haben mithilfe von molekularen Computersimulationen eines einfachen Modells gezeigt, dass Hydrationsfluktuationen in der hydrophoben Bindungstasche an die Dynamik des Liganden koppeln und damit seine Bindungsrate beeinflussen. Da die Wasserfluktuationen wiederum durch die Geometrie und Hydrophobizität der Bindungstasche beeinflusst werden, entsteht die Möglichkeit, kontrollierte Fluktuation zu kreieren, um die Bindungsraten des Liganden zu steuern. In dieser Arbeit wird diese Perspektive mithilfe eines theoretischen Multiskalenansatzes für prototypische Schlüssel-Schloss-Systeme aufgegriffen. Wir untersuchen den Einfluss der physikochemischen Eigenschaften der Bindungstasche auf die Diffusivität und die Bindungsraten des Liganden, und wie die Orientierung eines anisotropen Liganden an die Hydrationsfluktuationen der Tasche koppelt. Damit stellen wir fest, dass kleine Änderungen der Taschentiefe eine extreme Beschleunigung der Bindungsraten bewirken kann und, dass gleichzeitig die Bindung in konkave Taschen vorteilhaft für die Reorientierungsdynamik des Liganden ist. Die Resultate dieses Projekts sollen somit helfen, maßgeschneiderte Lösungen für funktionale „Host-Guest“-Systeme sowie pharmazeutische Moleküle in biomedizinischen Anwendungen zu entwickeln.
The association of small molecules (ligands) to hydrophobic binding pockets plays an integral role in biochemical molecular recognition and function, as well as in various self-assembly processes in the physical chemistry of aqueous solutions. While the investigation of water contributions to the binding free energy (affinity) in equilibrium has attracted a great deal of attention in the last decade, little is known about the role of water in determining the rates of binding and kinetic mechanisms. For instance, what are the nanoscale water effects on ligand diffusion close to the hydrophobic docking site, and how can they be steered by the chemical composition of the pocket? Recent studies used molecular simulations of a simple prototypical pocket-ligand model to show that hydration fluctuations within the binding pocket can couple to the ligand dynamics and influence its binding rates. Since the hydration fluctuations, in turn, can be modified by the pocket’s geometry and hydrophobicity, the possibility exists to create well-controlled solvent fluctuations to steer the ligand’s binding rates. In this work, we pick up this appealing notion employing a theoretical multi-scale approach of a generic key-lock system in aqueous solution. We explore the influence of the physicochemical properties of the pocket on local ligand diffusivities and binding rates and demonstrate how the orientation of a (non-spherical) ligand couples to a pocket’s hydration fluctuations. We find that minor modulation in pocket depth can drastically speed up the binding rate and that, concurrently, binding to molded binding sites is advantageous for the rotational dynamics of the ligand. The results and discussion of this work shall, therefore, imply generic design principles for tailored solutions of functional host-guest systems as well as optimized drugs in biomedical applications.

From August 1996 through September 1997 eleven fixed stations were sampled monthly in January, March , April , July, August, September, and November and fortnightly in May and June for the purposes of establishing baseline conditions present in Lake Texoma as related to U.S. Army Corps of Engineers chloride control activities in the upper Wichita River, Texas. Five reservoir zones were identified a priori using historical chloride concentration data and include the Red River Zone (RRZ), Red River Transition Zone (RRTZ), Main Lake Body (MLB), Washita River Transition Zone (WRTZ), and Washita River Zone (WRZ) in order of decreasing chloride concentration. The existence of the WRTZ is not supported here, however the Big Mineral Arm in the RRTZ was observed to be highly independent of the mixing patterns observed in the RRTZ and was treated post priori separately from the RRTZ. Spatial and temporal comparisons between reservoir zones were performed on seventeen (17) physicochemical parameters from each of the eleven sampling stations and phytoplankton count data from one sampling station within each reservoir zone and physicochemical parameters were observed to exhibit a fixed spatial gradient. Strong density gradients throughout the reservoir were observed to occur in conjunction with vertical stratification of the water column. Stratification stability at individual stations was attributable to both thermal and salinity density gradients throughout the period of stratification with the degree to which stratification is thermally or chemically induced influenced by inter-annual variability in hydraulic residence time. Hypolimnetic oxygen depletion rates were also observed to be affected by changes in hydraulic residence time with a long-term trend of decreasing relative areal hypolimnetic oxygen rates detected between the 1970s and 1990s. The algal assemblage present in Lake Texoma is dominated by the Cyanophyta, which comprises 82.1 % of the assemblage total standing crop with one species, Microcystis incerta, comprising 57.0 % of the assemblage total standing crop and is typical of a temperate eutrophic lake. The algal assemblage was affected more by temporal dynamics rather than spatial dynamics with variance observed in the algal assemblage attributable to physicochemical factors which vary through time.

Sediment delivery is a major problem in the Green River, Kentucky, home of 71 of the state’s 103 known mussel species and 151 fish species. The river also provides water for many of its surrounding counties. This research focuses on how suspended sediment loads, grain size, and sediment concentration during runoff events are related to watershed characteristics. The research characterized suspended sediment loads, grain size, and sediment concentration during runoff events and how they were related to watershed characteristics such as hydro-climatic regime, watershed size, geology and soils, topography and landuse conditions and land cover conditions. The study focused on Brush Creek and Pitman Creek watersheds in the Upper Green River Basin. This research can help in the planning and development of effective environmental strategies by screening out mitigation measures that would not be effective for implementation to minimize sediment load and suspended sediment concentration in the Green River, thereby improving the water quality of the river. Water quality was monitored using data sondes positioned at selected sites in the two watersheds. Water samples were collected during turbidity thresholds of 100 NTU and analyzed for suspended sediment concentrations. Regression models between ‘discharge and stage’ and also between ‘average turbidity and suspended sediment concentration’ were formulated and load estimates were made and compared. Four sets of samples were collected, two at Brush Creek on 11 April (Brush Creek’s event 1) and 3 May (Brush Creek’s event 2) and the other two at Pitman Creek on the 12 February (Pitman Creek’s event 1) and 3 March (Pitman Creek’s event 2) all in the year 2008. The suspended sediment samples collected for all four events were well graded but had relatively more silt than clay and sand. This could be due to the fact that more time and energy was needed to break the bonds in clay minerals or particles and also to the fact that more energy was also needed to transport sand compared to silt. Brush Creek watershed’s particles had smaller grain sizes than Pitman Creek watershed’s particles. All four events showed clockwise hysteresis indicating that most of the sediments from both watersheds during the events were derived from the bed and banks of the channel or area adjacent to the channel. The 11 April event (Brush Creek’s event 1) produced an estimated load of 1.1 x 105 kg and a sediment yield of 5.3 x 102 kg/km2. The 3 May event (Brush Creek’s event 2) produced an estimated load of 3.8 x 104 kg and a sediment yield of 1.8 x 102 kg/km2. Brush Creek watershed’s estimated load for the period compared was 4.9 x 105 kg and a sediment yield of 2.3 x 103 kg/km2 (53 kg/km2/day). The 12 February event (Pitman Creek’s event 1) produced an estimated load of 2.9 x 105 kg and a sediment yield of 8.4 x 102 kg/km2. The 3 March event (Pitman Creek’s event 2) produced an estimated load of 5.7 x 105 kg and a sediment yield of 1.6 x 103 kg/km2. Pitman Creek watershed’s estimated load for the period compared was 1.1 x 106 kg and a sediment yield of 3.1 x 103 kg/km2 (71 kg/km2/day). Pitman Creek watershed’s higher number of stream network per unit area, its high elevation and relief, its high percentage of erodible soil per unit area, its lesser area of protection of erodible soil by its vegetation compared to Brush Creek watershed’s are responsible for its higher sediment load and yield.

In this licentiate thesis the luminescence properties of two flexible conjugated dyes have been studied. The first, Pt1, is a platinum(II) acetylide chromophore used in optical power limiting materials. The second is a set of optical probes known as luminescent conjugated oligothiophenes (LCOs), which are used to detect and characterize the protein structures associated with amyloid diseases such as Alzheimer’s disease. MM3 and CHARMM force field parameters have been derived for the Pt1 chromophore and LCOs, respectively, based on potential energy surface references calculated at the density functional theory (DFT)/B3LYP level of theory. The parameters have been used to perform room temperature molecular dynamics simulations of the chromophores in solvent, where tetrahydrofuran was used for Pt1 and water for the LCOs. Conformationally averaged absorption spectra were obtained, based on response theory calculations at the time-dependent DFT(TDDFT)/CAM-B3LYP level of theory for a selection of structures from the simulations. For one of the LCOs, p-HTAA, force field parameters were also created describing the dominant first excited state, based on TDDFT/B3LYP reference potential energy surfaces. These were used for molecular dynamics simulations of the chromophore in the excited state, allowing the creation of an emission spectrum. A theoretically obtained Stokes shift of 112 nm could be computed based on the absorption and emission spectra, which is in good agreement with the experimental value of 124 nm. In addition, a quantum mechanics/molecular mechanics study of the effects of solvation on the absorption properties of the p-HTAA chromophore in water has been conducted, resulting in two models for including these effects in the averaged spectra. The first includes explicit water molecules in the form of point charges and polarizable dipole moments, and results in an absorption wavelength that is blueshifted by 2 nm from a high quality reference calculation. The second model involves the complete removal of the solvent as well as the ionic groups of the chromophore. The resulting absorption wavelength is blueshifted by an additional 4 nm as compared to the first model, but requires only one fifth of the computational resources.

The thesis presents detailed results of theoretical analyses based on extensive computer simulation studies with an aim to explore, quantify whenever possible, and understand structure and dynamics of polymers and proteins in several complex solvents. In order to make the Thesis coherent, we also study certain aspects of binary mixtures. Based on the phenomena studied, the thesis has been divided into four major parts: I. Dynamics of biological water: Distance dependent variation of dielectric constants in aqueous protein solutions II. Temperature dependent study of structural transformations in aqueous binary mixtures III. Conformation and dynamics of polymers in solution: Role of aqueous binary mixtures IV. Conformational change and unfolding dynamics of proteins: Role of sol-vent environment The above mentioned four parts have further been divided into thirteen chapters. In the following we provide a brief chapter-wise outline of the thesis. Part I consists of two chapters, where we focus on the study of dynamics of biological water and distance dependent variation of static and dynamic proper-ties (including dielectric constant) of water near different proteins. To start with, chapter 1 provides an introduction to the structure and dynamics of biological water. Here we discuss different experimental studies; including dielectric relaxation, NMR and salvation dynamics those explore the bimolecular hydration dynamics in great detail. We also discuss the wide range of computer simulation and theoretical studies that have been carried out to understand the dynamical behaviour of biological water. In chapter 2, we present our molecular dynamics simulation study to ex-plore the distance dependent static and dynamic behaviour of biological water near four different protein surfaces. Proteins are known to have large permanent dipole moments that can influence structure and dynamics of even distant water molecules. Therefore, distance dependence of polarization punctuation can provide important insight into the nature of biological water. We explore these aspects by studying aqueous solutions of four different proteins of different char-acteristics and varying sizes. We find that the calculated dielectric constants of the systems show a noticeable increment in all the cases compared to that of neat water. Total dipole moment auto time correlation function of water is found to be sensitive to the nature of the protein. We also define and calculate the effective dielectric constant of successive layers and find that the layer adjacent to protein always has significantly lower value (∼ 50). However, progressive layers exhibit successive increment of dielectric constant, finally reaching a value close to that of bulk 4–5 layers away. Theoretical analysis providing simple method for calculation of shellwise local dielectric constant and implication of these findings are elaborately discussed in this chapter. Part II deals with the temperature dependent study of aqueous DMSO and ethanol solutions and consists of three chapters. Chapter 3 provides a general introduction to the non-ideality (deviation from Raoult’s law) encountered in different binary mixtures. We discuss different theoretical models for treatment of binary mixtures. Finally we provide a systematic study about the non-ideality observed in aqueous binary mixtures. Here we discuss the anomalies observed in such systems and carry out a brief survey on the existing ideas of structural transformations associated with the solvation of a foreign molecule in water. In chapter 4, we discuss the results of temperature dependent study of struc-tural and dynamic properties of aqueous dimethyl sulfoxide (DMSO) mixture. It is now well-known that aqueous DMSO mixture exhibits signature of perco-lation driven structural aggregation at a mole fraction range xDMSO ≈ 0.15. We study the structural and dynamical change in this binary mixture below and above the percolation threshold along with decreasing temperature. Significant change in the molecular structure of DMSO as well as that of water is observed above the percolation threshold at a lower temperature, particularly at 200K. The structural arrangement of the DMSO molecules is found to be progressively more ordered with increasing DMSO concentration and decreasing temperature. On the other hand, water structure is found to be significantly deviated from tetrahedral arrangement in presence of DMSO clusters even at low temperature. The dynamics of water is also found to be considerably affected with increase of concentration and lowering of temperature. Similar phenomenon is observed for another amphiphilic molecule, ethanol, and has been discussed in chapter 5. Aqueous ethanol mixture is a widely studied solvent, both experimentally and using computer simulations. All the studies indicate several distinct salvation regimes. In recent molecular dynamics simulation studies, the reason for formation of micro-aggregates of ethanol is again attributed to percolation driven structural transformation. We carry out a temperature dependent study of water-ethanol binary mixture, particularly at low ethanol concentration to understand the molecular origin of such structural transformation. We find that the structural arrangement of ethanol as well as water molecules is similarly affected as that of DMSO with lowering of temperature. However, dynamics of water molecules in aqueous ethanol solution is found to be marginally affected, unlike the case of aqueous DMSO solution. We discuss the microscopic reason for such behaviour in a detailed manner. In Part III, we discuss the dynamics of linear polymer chains in different aqueous binary mixtures. Here we have three chapters. In chapter 6, we carry out a brief survey of the existing theories of polymers in solution. We discuss the quality of solvents depending on the preferred interactions between the polymer and the solvent or the polymer with its own. We also discuss the celebrated Flory-Huggins theory. We derive the expression of free energy of the Flory-Huggins theory in terms of the volume fraction of monomer and solvent molecules. In chapter 7, we discuss the results of our study of polymer dynamics in aqueous DMSO solution. We find that at a mole fraction 0.05 of DMSO (xDMSO ≈ 0.05) in aqueous solution, a linear polymer chain of intermediate length (n=30) adopts collapsed conformation as the most stable conformational state. The same chain exhibits an intermittent oscillation between the collapsed and the extended coiled conformations in neat water. Even when the mole fraction of DMSO in the bulk is 0.05, the concentration of the same in the first hydration layer around the polymer is found to be as large as 17 %. Formation of such hydrophobic environment around the hydrocarbon chain may be viewed as the reason for the collapsed conformation gaining additional stability. We find a second anomalous behaviour to emerge near xDMSO ≈ 0.15 that is attributed to the percolation driven structural aggregation of DMSO that lowers the relative concentration of the DMSO molecules in the hydration layer. In chapter 8, we carry out similar study of linear polymer chain in water– ethanol binary mixture. In this case also, we find a sudden collapse of the poly-merat xEtOH ≈ 0.05. Since ethanol molecules are known to form micro-aggregates in this concentration range, stability of collapsed state of polymer at this con-centration is anticipated to be correlated to this phenomenon. In fact, a purely hydrophobic polymer chain, in its collapsed form is anticipated to assist in the formation of spanning cluster comprised of hydrophobic ethyl groups at this concentration range thereby facilitating the percolation transition. We discuss these prospects in this chapter. Part IV deals with the solvent sensitivity to the conformational change and unfolding dynamics of protein. Part IV consists of five chapters. In chapter 9, we develop an understanding of protein folding and unfolding dynamics by discussing the fundamental theories developed in the last few decades. We also discuss the major role of solvents in stabilizing or destabilizing the native, ordered state. In chapter 10, we present a detailed study of unfolding of a small protein, chicken villin headpiece (HP36) in water-ethanol binary mixture, using molecular dynamics simulations. The prime objective of this work is to explore the sensitivity of protein dynamics towards increasing concentration of the cosolvent and unravel essential features of intermediates formed in the unfolding path-way. In water–ethanol binary mixtures, HP36 is found to unfold partially, under ambient conditions, that otherwise requires temperature as high as ∼ 600K to denature in pure aqueous solvent. The study unravels certain interesting aspects about the pathway of unfolding, guided by the formation of unique intermediates. Unfolding is initiated by the separation of hydrophoic core comprising three phenylalanine residues (Phe7, Phe11, Phe18). This separation initiates the melting of the helix2 of the protein. However, with an increase of cosolvent concentration different partially unfolded intermediates are found to be formed. We attribute the emergence of such partially unfolded states to the preferential solvation of hydrophobic residues by the ethyl groups of ethanol. We explore and subsequently quantify the detailed dynamics of unfolding in water-ethanol that appear to be more complex and sensitive to solvent composition. With an aim to develop a general understanding of the role of water–ethanol binary mixture in facilitating anomalous conformational dynamics of proteins, we carry out combined theoretical and experimental studies to explore detailed structural change of a larger protein, Myoglobin with increasing ethanol concentration. These studies are described in chapter 11. In agreement with our pre-vious observations, we identify in this case two well-defined structural regimes, one at xEtOH ≈ 0.05 and the other at xEtOH ≈ 0.25, characterized by formation of distinct partially folded conformations and separated by a unique partially unfolded intermediate state at xEtOH ≈ 0.15. We also find non-monotonic com-position dependence of (i) radius of gyration (ii) long range contact order (iii) residue specific solvent accessible surface area of tryptophan (iv) circular dichro-ism spectra and UV-absorption peaks. Multiple structural transformations, well-known in water-ethanol binary mixture, appear to have considerably stronger effects on the conformation and dynamics of protein Myoglobin. In chapter 12, we explore the free energy surface of unfolding pathway through umbrella sampling, for the small globular alpha-helical protein chicken-villin headpiece (HP36) in three different solvent conditions (water, xDMSO ≈ 0.15 and xDMSO ≈ 0.3). Recently established as a facilitator of helix melting, DMSO is found to be a good denaturant for HP36 and at a mole fraction of xDMSO ≈ 0.3, complete melting of the protein is ensured. The unfolding proceeds through initial separation or melting of the same aggregated hydrophobic core that com-prises three phenylalanine residues (Phe7, Phe11 and Phe18) accompanied by simultaneous melting of the helix2. Unfolding is found to be a multistage process involving crossing of three consecutive minima and two barriers at the initial stage. At a molecular level, Phe18 is observed to reorient itself towards other hy-drophobic grooves to stabilize the intermediate states. We identify the configuration of intermediates in all the solvent conditions which are found to be unique for the corresponding minima with similar structural arrangement. Consider-able softening of the barriers is observed with increasing DMSO concentration. Higher concentration of DMSO tunes the unfolding pathway by destabilizing the third minimum and stabilizing the second one, indicating the development of solvent modified, less rugged pathway. Chapter 13 provides a detailed microscopic mechanism of DMSO induced unfolding of HP36. We analyze the free energy contours of the protein HP36, obtained from molecular dynamics simulation in xDMSO ≈ 0.15 and xDMSO ≈ 0.3. The most probable intermediates obtained from the free energy contours are found to be similar to those obtained from umbrella sampling which again sup-ports the fact that the melting proceeds through formation of a series of unique intermediates. We characterize the preferential hydrophobic salvation of the hydrophobic core that drives the melting of secondary structure, by calculating time dependent radial distribution function and identifying the formation of strong orientation order between methyl groups of DMSO and phenyl alanine residues. Finally we employ Kramer’s rate equation to calculate the rate of bar-rier crossing that reveals significantly faster rate of unfolding with increasing DMSO concentration that is in agreement with simulation results. Whenever possible, we have discussed the scope of future work at the end of each chapter.

The thesis presents detailed results of theoretical analyses based on extensive computer simulation studies with an aim to explore, quantify whenever possible, and understand structure and dynamics of polymers and proteins in several complex solvents. In order to make the Thesis coherent, we also study certain aspects of binary mixtures. Based on the phenomena studied, the thesis has been divided into four major parts: I. Dynamics of biological water: Distance dependent variation of dielectric constants in aqueous protein solutions II. Temperature dependent study of structural transformations in aqueous binary mixtures III. Conformation and dynamics of polymers in solution: Role of aqueous binary mixtures IV. Conformational change and unfolding dynamics of proteins: Role of sol-vent environment The above mentioned four parts have further been divided into thirteen chapters. In the following we provide a brief chapter-wise outline of the thesis. Part I consists of two chapters, where we focus on the study of dynamics of biological water and distance dependent variation of static and dynamic proper-ties (including dielectric constant) of water near different proteins. To start with, chapter 1 provides an introduction to the structure and dynamics of biological water. Here we discuss different experimental studies; including dielectric relaxation, NMR and salvation dynamics those explore the bimolecular hydration dynamics in great detail. We also discuss the wide range of computer simulation and theoretical studies that have been carried out to understand the dynamical behaviour of biological water. In chapter 2, we present our molecular dynamics simulation study to ex-plore the distance dependent static and dynamic behaviour of biological water near four different protein surfaces. Proteins are known to have large permanent dipole moments that can influence structure and dynamics of even distant water molecules. Therefore, distance dependence of polarization punctuation can provide important insight into the nature of biological water. We explore these aspects by studying aqueous solutions of four different proteins of different char-acteristics and varying sizes. We find that the calculated dielectric constants of the systems show a noticeable increment in all the cases compared to that of neat water. Total dipole moment auto time correlation function of water is found to be sensitive to the nature of the protein. We also define and calculate the effective dielectric constant of successive layers and find that the layer adjacent to protein always has significantly lower value (∼ 50). However, progressive layers exhibit successive increment of dielectric constant, finally reaching a value close to that of bulk 4–5 layers away. Theoretical analysis providing simple method for calculation of shellwise local dielectric constant and implication of these findings are elaborately discussed in this chapter. Part II deals with the temperature dependent study of aqueous DMSO and ethanol solutions and consists of three chapters. Chapter 3 provides a general introduction to the non-ideality (deviation from Raoult’s law) encountered in different binary mixtures. We discuss different theoretical models for treatment of binary mixtures. Finally we provide a systematic study about the non-ideality observed in aqueous binary mixtures. Here we discuss the anomalies observed in such systems and carry out a brief survey on the existing ideas of structural transformations associated with the solvation of a foreign molecule in water. In chapter 4, we discuss the results of temperature dependent study of struc-tural and dynamic properties of aqueous dimethyl sulfoxide (DMSO) mixture. It is now well-known that aqueous DMSO mixture exhibits signature of perco-lation driven structural aggregation at a mole fraction range xDMSO ≈ 0.15. We study the structural and dynamical change in this binary mixture below and above the percolation threshold along with decreasing temperature. Significant change in the molecular structure of DMSO as well as that of water is observed above the percolation threshold at a lower temperature, particularly at 200K. The structural arrangement of the DMSO molecules is found to be progressively more ordered with increasing DMSO concentration and decreasing temperature. On the other hand, water structure is found to be significantly deviated from tetrahedral arrangement in presence of DMSO clusters even at low temperature. The dynamics of water is also found to be considerably affected with increase of concentration and lowering of temperature. Similar phenomenon is observed for another amphiphilic molecule, ethanol, and has been discussed in chapter 5. Aqueous ethanol mixture is a widely studied solvent, both experimentally and using computer simulations. All the studies indicate several distinct salvation regimes. In recent molecular dynamics simulation studies, the reason for formation of micro-aggregates of ethanol is again attributed to percolation driven structural transformation. We carry out a temperature dependent study of water-ethanol binary mixture, particularly at low ethanol concentration to understand the molecular origin of such structural transformation. We find that the structural arrangement of ethanol as well as water molecules is similarly affected as that of DMSO with lowering of temperature. However, dynamics of water molecules in aqueous ethanol solution is found to be marginally affected, unlike the case of aqueous DMSO solution. We discuss the microscopic reason for such behaviour in a detailed manner. In Part III, we discuss the dynamics of linear polymer chains in different aqueous binary mixtures. Here we have three chapters. In chapter 6, we carry out a brief survey of the existing theories of polymers in solution. We discuss the quality of solvents depending on the preferred interactions between the polymer and the solvent or the polymer with its own. We also discuss the celebrated Flory-Huggins theory. We derive the expression of free energy of the Flory-Huggins theory in terms of the volume fraction of monomer and solvent molecules. In chapter 7, we discuss the results of our study of polymer dynamics in aqueous DMSO solution. We find that at a mole fraction 0.05 of DMSO (xDMSO ≈ 0.05) in aqueous solution, a linear polymer chain of intermediate length (n=30) adopts collapsed conformation as the most stable conformational state. The same chain exhibits an intermittent oscillation between the collapsed and the extended coiled conformations in neat water. Even when the mole fraction of DMSO in the bulk is 0.05, the concentration of the same in the first hydration layer around the polymer is found to be as large as 17 %. Formation of such hydrophobic environment around the hydrocarbon chain may be viewed as the reason for the collapsed conformation gaining additional stability. We find a second anomalous behaviour to emerge near xDMSO ≈ 0.15 that is attributed to the percolation driven structural aggregation of DMSO that lowers the relative concentration of the DMSO molecules in the hydration layer. In chapter 8, we carry out similar study of linear polymer chain in water– ethanol binary mixture. In this case also, we find a sudden collapse of the poly-merat xEtOH ≈ 0.05. Since ethanol molecules are known to form micro-aggregates in this concentration range, stability of collapsed state of polymer at this con-centration is anticipated to be correlated to this phenomenon. In fact, a purely hydrophobic polymer chain, in its collapsed form is anticipated to assist in the formation of spanning cluster comprised of hydrophobic ethyl groups at this concentration range thereby facilitating the percolation transition. We discuss these prospects in this chapter. Part IV deals with the solvent sensitivity to the conformational change and unfolding dynamics of protein. Part IV consists of five chapters. In chapter 9, we develop an understanding of protein folding and unfolding dynamics by discussing the fundamental theories developed in the last few decades. We also discuss the major role of solvents in stabilizing or destabilizing the native, ordered state. In chapter 10, we present a detailed study of unfolding of a small protein, chicken villin headpiece (HP36) in water-ethanol binary mixture, using molecular dynamics simulations. The prime objective of this work is to explore the sensitivity of protein dynamics towards increasing concentration of the cosolvent and unravel essential features of intermediates formed in the unfolding path-way. In water–ethanol binary mixtures, HP36 is found to unfold partially, under ambient conditions, that otherwise requires temperature as high as ∼ 600K to denature in pure aqueous solvent. The study unravels certain interesting aspects about the pathway of unfolding, guided by the formation of unique intermediates. Unfolding is initiated by the separation of hydrophoic core comprising three phenylalanine residues (Phe7, Phe11, Phe18). This separation initiates the melting of the helix2 of the protein. However, with an increase of cosolvent concentration different partially unfolded intermediates are found to be formed. We attribute the emergence of such partially unfolded states to the preferential solvation of hydrophobic residues by the ethyl groups of ethanol. We explore and subsequently quantify the detailed dynamics of unfolding in water-ethanol that appear to be more complex and sensitive to solvent composition. With an aim to develop a general understanding of the role of water–ethanol binary mixture in facilitating anomalous conformational dynamics of proteins, we carry out combined theoretical and experimental studies to explore detailed structural change of a larger protein, Myoglobin with increasing ethanol concentration. These studies are described in chapter 11. In agreement with our pre-vious observations, we identify in this case two well-defined structural regimes, one at xEtOH ≈ 0.05 and the other at xEtOH ≈ 0.25, characterized by formation of distinct partially folded conformations and separated by a unique partially unfolded intermediate state at xEtOH ≈ 0.15. We also find non-monotonic com-position dependence of (i) radius of gyration (ii) long range contact order (iii) residue specific solvent accessible surface area of tryptophan (iv) circular dichro-ism spectra and UV-absorption peaks. Multiple structural transformations, well-known in water-ethanol binary mixture, appear to have considerably stronger effects on the conformation and dynamics of protein Myoglobin. In chapter 12, we explore the free energy surface of unfolding pathway through umbrella sampling, for the small globular alpha-helical protein chicken-villin headpiece (HP36) in three different solvent conditions (water, xDMSO ≈ 0.15 and xDMSO ≈ 0.3). Recently established as a facilitator of helix melting, DMSO is found to be a good denaturant for HP36 and at a mole fraction of xDMSO ≈ 0.3, complete melting of the protein is ensured. The unfolding proceeds through initial separation or melting of the same aggregated hydrophobic core that com-prises three phenylalanine residues (Phe7, Phe11 and Phe18) accompanied by simultaneous melting of the helix2. Unfolding is found to be a multistage process involving crossing of three consecutive minima and two barriers at the initial stage. At a molecular level, Phe18 is observed to reorient itself towards other hy-drophobic grooves to stabilize the intermediate states. We identify the configuration of intermediates in all the solvent conditions which are found to be unique for the corresponding minima with similar structural arrangement. Consider-able softening of the barriers is observed with increasing DMSO concentration. Higher concentration of DMSO tunes the unfolding pathway by destabilizing the third minimum and stabilizing the second one, indicating the development of solvent modified, less rugged pathway. Chapter 13 provides a detailed microscopic mechanism of DMSO induced unfolding of HP36. We analyze the free energy contours of the protein HP36, obtained from molecular dynamics simulation in xDMSO ≈ 0.15 and xDMSO ≈ 0.3. The most probable intermediates obtained from the free energy contours are found to be similar to those obtained from umbrella sampling which again sup-ports the fact that the melting proceeds through formation of a series of unique intermediates. We characterize the preferential hydrophobic salvation of the hydrophobic core that drives the melting of secondary structure, by calculating time dependent radial distribution function and identifying the formation of strong orientation order between methyl groups of DMSO and phenyl alanine residues. Finally we employ Kramer’s rate equation to calculate the rate of bar-rier crossing that reveals significantly faster rate of unfolding with increasing DMSO concentration that is in agreement with simulation results. Whenever possible, we have discussed the scope of future work at the end of each chapter.

The thesis presents detailed results of theoretical analyses based on extensive computer simulation studies with an aim to explore, quantify whenever possible, and understand the collective excitations, relaxation processes and temperature dependent phase separation kinetics in several binary mixtures. We also investigate the structure and dynamics of water in the vicinity of several biologically active proteins and small hydrophobes. Based on the phenomena studied the thesis has been divided into four major parts I. Collective excitations and ultrafast solvation dynamics in binary mixtures II. Non-equilibrium solvation dynamics in binary mixture: Composition dependence of non-linear relaxation III.Nanoscale heterogeneous phase separation kinetics in binary mixtures: Multistage dynamics IV.Spatial dependence of dielectric constant in protein-water systems and hydrophobic hydration driven self-assembly of hydrophobic molecules in water: Role of nucleation

"November 2002."
Thesis (Ph.D.)--Chinese University of Hong Kong, 2002.
Includes bibliographical references (p. 206-213).
Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web.
Mode of access: World Wide Web.
Abstracts in English and Chinese.

The thesis contains theoretical studies of the structure and dynamics in different complex systems. Depending on the systems and properties of interest we divide the thesis into five parts. In the first part, we study chemical dynamics in nanoconfined water. Here we primarily focus on the dielectric properties of dipolar fluids confined inside nano-containers of various sizes and shapes. We discover an extremely slow convergence of the static dielectric constant (ε) of water with the size of the nanospheres. Our studies reveal an ultrafast relaxation of the collective orientation of water which is absent in the Stockmayer fluid. We connect this anomaly to the substantially low value of the Kirkwood g-factor for spherically confined water. We extrapolate the values of ε to obtain its true value in the thermodynamic limit which corroborates well with the values in periodic systems. We perform molecular dynamics simulations with three different liquid-surface interactions to study the surface effects. The dielectric response of water under becomes anisotropic in non-spherical confinements, namely, cylindrical and slab geometries. Because of the difference in the dielectric boundary conditions along the different directions, the eigenvalues of the dielectric tensor becomes unequal. We derive the fluctuation formulae for the anisotropic dielectric constants. For the cylindrical geometry, we find that the axial component (εz) and the perpendicular component (εx/y) converge to the bulk value, with the diameter of the nanotube, in an opposite manner. εx/y shows relatively slower convergence starting from a lower value whereas εz shows faster convergence starting from a higher value. For the slab system, the parallel component (ε∥) does not show much deviation from the bulk value. On the contrary, the perpendicular component (ε⊥) exhibits extremely low values for smaller systems and shows a slow convergence toward bulk. Interestingly, in the slab geometry, the dielectric relaxation along the perpendicular direction becomes ultrafast with pronounced oscillations. Our results match well with recent dielectric microscopy experiments. We perform a constrained Ising model-based analysis and to understand the inwardly propagating destructions among correlations. In addition to the above, we study the heterogeneous dynamics of water inside nano-enclosures of different shapes. We investigate the position-dependent solvation of model ionic/dipolar probes and find that the slow components of solvation show highly non-monotonic behaviour with the distance of the probe from the surface. To study the static and dynamical heterogeneity, we obtain the non-Gaussian parameter [α2(t)] and non-linear density response function [χ4(t)]. α2(t) shows an anomalous long-time growth for non-spherical systems which we attribute to the slow dynamics of water along the non-periodic direction(s). In the second part, we focus on the chemical dynamics in small-sized (~μm) droplets that exhibit noticeably different chemistry than bulk water. Several chemical reactions show markedly enhanced rates in the droplet media. Here we present a generalized theoretical model and analytically solve the adjoint equations for two- and three-dimensional systems. We obtain exact expressions for the mean search time (MST) that is found to be proportional to R2/D [R=radius, D=relative diffusion constant]. We carry out Brownian dynamics simulations and show that the MST of reactive partner search in droplets is orders of magnitude smaller than that in the bulk. As the experiments often use an external electric field to charge the droplets, we study the effect of ions and electric fields on the bond dissociation energy. We find that the presence of an ion or electric field weakens the bond and enhances the intrinsic reaction rate. Our results describe the interplay between diffusion control and activation controlled processes. In the third part, we study the dynamics of interfacial water molecules in the biomolecular hydration layers. Here we first aim to resolve a long-standing controversy regarding the timescale of water dynamics in the protein hydration layer, that is, solvation dynamics and dielectric relaxation finds substantial slow relaxation whereas NMR experiments find retardation only by a factor of 2-3. To this goal, we obtain distributions of single-particle relaxation timescales and show that the average values obtained from experiments hide the true picture. To our surprise, we find the existence of both faster and slower than bulk water molecules in the hydration layer. We unravel the origin of disparate timescales (from sub-100 fs to hundreds of ps) observed in the solvation dynamics of natural probe tryptophan tagged to three different proteins- Lysozyme, Myoglobin, and sweet protein Monellin. We show that the neighbourhood charged residues and the intrinsic side-chain fluctuations contribute to the observed slow dynamics. We further decompose the response into protein core, side-chains, and water contributions to study the nature of coupling. We find surprising anti-correlation between the energy fluctuations of protein and water. Our simulation results support the widely discussed protein-solvent slaving picture developed from earlier Mössbauer spectroscopy experiments. We also study the origin of the power law decay observed in DNA solvation dynamics. We employ the Oosawa model, continuum model, mode coupling theory, and continuous time random walk based analyses to unearth the effect of counterion motions. We study the solvation dynamics of DNA bases and a minor groove bound probe. In the fourth part, we characterize the various protonated forms of metformin hydrochloride (MET) by employing computational and spectroscopic techniques. We develop an AMBER based force-field for three protonation states of MET and validate them against available experimental results. We use this force-field to study the interaction of MET with double-stranded B-DNAs. As there is evidence of anti-tumour and anti-cancer activity of MET, we aim to understand its mode of binding with DNA. We employ metadynamics based advanced sampling techniques to obtain the free energy landscape of the binding process. We find that MET prefers AT-rich minor grooves through non-intercalative mode of binding. We confirm these claims from fluorescence spectroscopy and circular dichroism experiments. In the fifth and last part of the thesis, we study the structure and aggregation of insulin oligomers (dimer and hexamer) in water and water-ethanol binary mixtures. Insulin is biologically active in its monomeric form but gets stored in the pancreas as hexamers. The inter-conversion between monomer and hexamer occurs via dimeric intermediates. Here we present the structural analysis of insulin hexamer in water and water-ethanol binary mixture by using atomistic molecular dynamics and X-ray crystallography. We find that the water molecules trapped inside the central hydrophilic cavity of hexamer play a central role in sustaining the robust barrel-shaped structure. The presence of ethanol (even in lower concentrations) deforms the hexameric assembly. Next, we study the energetics of the insulin dimer association/dissociation process. We obtain the free energy landscape from parallel tempering metadynamics simulations in a well-tempered ensemble with respect to two collective variables- inter-monomeric distance and the number of inter-monomeric contacts. We find that the activation barrier of dissociation drastically decreases in the presence of 5% and 10% (v/v) ethanol. We attribute this effect to the preferential solvation of the dimer forming hydrophobic surface of the monomers that results in the destruction of inter-monomeric hydrogen bonding. We analyze the evolving structures along the minimum energy pathway and establish the role of the solvent.

The thesis, which contains nine chapters, reports extensive large scale atomistic molecular dynamics (MD) simulation studies of water structure and dynamics at the surface of an anionic micelle, hydration layer of two proteins, and in the grooves of a 38-base pairs long DNA. Understanding the structure and dynamics of water molecules at the surfaces of self-organized assemblies and complex biological macromolecules has become a subject of intense research in recent times. Chapter 1 contains a brief overview of the biomolecular hydration dynamics. Relevant experimental, computational, and theoretical studies of biomolecular hydration and the time scales associated with the water dynamics are discussed. In Chapters 2 and 3, the structure, environment, energetics, and dynamics of constrained water molecules in the aqueous anionic micelle of cesium perfluorooctanoate (CsPFO) have been studied using large scale atomistic molecular dynamics simulations. Based on the number of hydrogen bond (HB) that interfacial water molecule makes with the polar head group (PHG) oxygen of the micelle, we find the existence of three kinds of water at the interface. We introduce a nomenclature to identify the species as IBW2 (form two HBs with two different PHG), IBW1 (form one HB with PHG), and IFW (no HB with PHG). Despite of possessing two strong w-PHG bonds, the concentration of the IBW2 species is rather low due to entropic effect. The ion solvation dynamics study at the interface shows the presence of a slow component, with a relaxation time 1-2 order of magnitude slower than that in the corresponding bulk solvent in agreement with the experimental results. Both the translational and orientational dynamics of the water molecules near the micellar surface is found to be much slower than those in the bulk. The HB between the PHG of the micelle and the water molecule has almost 13 times longer life time than that in the bulk between two tagged water molecules. In Chapter 4, we present results of extensive atomistic MD simulation studies of the structure and dynamics of aqueous protein solution of the toxic domain of Enterotoxin (1ETN) and the chicken villin headpiece sub-domain containing 36 amino acid residues (HP-36). Reduced water structure and the faster water dynamics around the active site of these proteins have been observed which may have biological significance. Chapter 5 presents an extensive atomistic molecular dynamics simulations study of water dynamics in the hydration layer of a 38 base long hydrated DNA duplex. The computed rotational time correlation function (TCF) of the minor groove water dipoles is found to be markedly non-exponential with a slow component at long time. The constrained water molecule is also found to exhibit anisotropic diffusion in both the major and minor grooves. At short-to-intermediate times, translational motion of water molecules in minor groove is sub-diffusive. Chapter 6 presents the study of water entropy in both the grooves DNA. The average values of the entropy of water at 300K in both the grooves of DNA are found to be significantly lower than that in bulk water. We propose that the configurational entropy of water in the grooves can be used as a measure of the mobility (or micro viscosity) of water molecules in a given domain. In Chapter 7, we study the specific DNA base-water hydrogen bond lifetime (HBLT) dynamics at the major and the minor grooves of a hydrated duplex. The base-water HBLT correlation functions are in general multi-exponential and the average lifetime depends significantly on the specificity of the DNA sequence. The average HBLT is longer in the minor groove than that in the major groove by almost a factor of 2. Chapter 8 presents the solvation dynamics of constituent bases of aqueous DNA duplex. The solvation TCFs of the four individual bases display highly non-exponential decay with time. An interesting negative cross-correlation between water and counterions is observed which makes an important contribution to relaxation at intermediate to longer times. In the concluding note, Chapter 9 presents a brief summary of the outcome of the thesis and suggests several relevant problems that may prove w orthwhile to be addressed in future

The thesis, which contains nine chapters, reports extensive large scale atomistic molecular dynamics (MD) simulation studies of water structure and dynamics at the surface of an anionic micelle, hydration layer of two proteins, and in the grooves of a 38-base pairs long DNA. Understanding the structure and dynamics of water molecules at the surfaces of self-organized assemblies and complex biological macromolecules has become a subject of intense research in recent times. Chapter 1 contains a brief overview of the biomolecular hydration dynamics. Relevant experimental, computational, and theoretical studies of biomolecular hydration and the time scales associated with the water dynamics are discussed. In Chapters 2 and 3, the structure, environment, energetics, and dynamics of constrained water molecules in the aqueous anionic micelle of cesium perfluorooctanoate (CsPFO) have been studied using large scale atomistic molecular dynamics simulations. Based on the number of hydrogen bond (HB) that interfacial water molecule makes with the polar head group (PHG) oxygen of the micelle, we find the existence of three kinds of water at the interface. We introduce a nomenclature to identify the species as IBW2 (form two HBs with two different PHG), IBW1 (form one HB with PHG), and IFW (no HB with PHG). Despite of possessing two strong w-PHG bonds, the concentration of the IBW2 species is rather low due to entropic effect. The ion solvation dynamics study at the interface shows the presence of a slow component, with a relaxation time 1-2 order of magnitude slower than that in the corresponding bulk solvent in agreement with the experimental results. Both the translational and orientational dynamics of the water molecules near the micellar surface is found to be much slower than those in the bulk. The HB between the PHG of the micelle and the water molecule has almost 13 times longer life time than that in the bulk between two tagged water molecules. In Chapter 4, we present results of extensive atomistic MD simulation studies of the structure and dynamics of aqueous protein solution of the toxic domain of Enterotoxin (1ETN) and the chicken villin headpiece sub-domain containing 36 amino acid residues (HP-36). Reduced water structure and the faster water dynamics around the active site of these proteins have been observed which may have biological significance. Chapter 5 presents an extensive atomistic molecular dynamics simulations study of water dynamics in the hydration layer of a 38 base long hydrated DNA duplex. The computed rotational time correlation function (TCF) of the minor groove water dipoles is found to be markedly non-exponential with a slow component at long time. The constrained water molecule is also found to exhibit anisotropic diffusion in both the major and minor grooves. At short-to-intermediate times, translational motion of water molecules in minor groove is sub-diffusive. Chapter 6 presents the study of water entropy in both the grooves DNA. The average values of the entropy of water at 300K in both the grooves of DNA are found to be significantly lower than that in bulk water. We propose that the configurational entropy of water in the grooves can be used as a measure of the mobility (or micro viscosity) of water molecules in a given domain. In Chapter 7, we study the specific DNA base-water hydrogen bond lifetime (HBLT) dynamics at the major and the minor grooves of a hydrated duplex. The base-water HBLT correlation functions are in general multi-exponential and the average lifetime depends significantly on the specificity of the DNA sequence. The average HBLT is longer in the minor groove than that in the major groove by almost a factor of 2. Chapter 8 presents the solvation dynamics of constituent bases of aqueous DNA duplex. The solvation TCFs of the four individual bases display highly non-exponential decay with time. An interesting negative cross-correlation between water and counterions is observed which makes an important contribution to relaxation at intermediate to longer times. In the concluding note, Chapter 9 presents a brief summary of the outcome of the thesis and suggests several relevant problems that may prove w orthwhile to be addressed in future

The first objective of this study was to investigate the role of an invasive grass species, Arundo donax (L.), on the hydrologic cycle. At a site on the Rio Grande in South Texas, we measured the gas exchange of carbon dioxide and water vapor at the leaf scale and structural characteristics, such as leaf area and shoot density, at the stand scale. In order to assess the effect of water availability, this study was conducted along transects perpendicular to the edge of the river along a potential moisture gradient. The second objective was to quantify the effect of two herbivores, an armored scale, Rhizaspidiotus donacis (Leonardi), and a stem-galling wasp, Tetramesa romana (Walker),on the photosynthetic and transpiration rates of A. donax. Leaf gas exchange measurements were made to determine the direction and magnitude of the effect on physiological processes and by what mechanisms any effects arose. Stands of A. donax used approximately 9.1 � 1.1 mm of water per day. This rate of water use was at the high end of the spectrum for plants. The major controls on stand scale transpiration were evaporative demand, leaf area index, and water availability. During two summer seasons, stand scale transpiration varied greatly, following the pattern of variability in precipitation, suggesting that recent rainfall constituted a significant proportion of the water taken up by this species. Herbivory by a stem-galling wasp and a sap-feeding scale, both separately and together, reduced the rates of leaf scale physiological processes in A. donax. The efficacy of the wasp was density dependent, and this herbivore reduced the carboxylation rate of Rubisco. The effect of the scale took approximately five months to manifest, which coincided with generation time. Scale reduced photosynthesis by decreasing the maximum rate of electron transport. When the two insects were both present, the effect of their herbivory seemed to be additive. These results will assist the responsible management agencies in evaluating the propriety of using one or both of the insect herbivores as biological control agents.