arXiv subjects

Biman Bagchi

Publications and source records attributed to Biman Bagchi.

At least 91 records · Page 5Linked to original sources

arXiv2014

A stochastic chemical dynamic approach to correlate autoimmunity and optimal vitamin-D range

Motivated by several recent experimental observations that vitamin-D could interact with antigen presenting cells (APCs) and T-lymphocyte cells (T-cells) to promote and to regulate different stages of immune response, we developed a coarse grained kinetic model in an attempt to quantify the role of vitamin-D in immunomodulatory responses. Our kinetic model, developed using the ideas of chemical network theory, leads to a system of nine coupled equations that we solve both by direct and by stochastic (Gillespie) methods. Both the analyses consistently provide detail information on the dependence of immune response to the variation of critical rate parameters. We find that although vitamin-D plays a negligible role in the initial immune response, it exerts a profound influence in the long term, especially in helping the system to achieve a new, stable steady state. The study explores the role of vitamin-D in preserving an observed bistability in the phase diagram (spanned by system parameters) of immune regulation, thus allowing the response to tolerate a wide range of pathogenic stimulation which could help in resisting autoimmune diseases. We also study how vitamin-D affects the time dependent population of dendritic cells that connect between innate and adaptive immune responses. Variations in dose dependent response in anti-inflammatory and pro-inflammatory T-cell populations to vitamin-D correlate well with recent experimental results. Our kinetic model allows for an estimation of the range of optimum level of vitamin-D required for smooth functioning of the immune system and for control of both hyper-regulation and inflammation. Most importantly, the present study reveals that an overdose or toxic level of vitamin-D or any steroid analogue could give rise to too large a tolerant response, leading to an inefficacy in adaptive immune function.

q-bio.MN↗

arXiv2014

A Comparative Study of Protein Unfolding in Aqueous Urea and DMSO Solutions: Surface Polarity, Solvent Specificity and Sequence of Secondary Structure Melting

Elucidation of possible pathways between folded (native) and unfolded states of a protein is a challenging task, as the intermediates are often hard to detect. Here we alter the solvent environment in a controlled manner by choosing two different co-solvents of water, urea and dimethyl sulphoxide (DMSO), and study unfolding of four different proteins to understand the respective sequence of melting by computer simulation methods. We indeed find interesting differences in the sequence of melting of alpha-helices and beta-sheets in these two solvents. For example, at 8M urea solution, beta-sheet parts of a protein is found to unfold preferentially, followed by the unfolding of alpha helices. In contrast, 8M DMSO solution unfolds alpha helices first, followed by the separation of beta-sheets for majority of proteins. Sequence of unfolding events in four different alpha/beta proteins and also in chicken villin head piece (HP-36) both in urea and DMSO solution demonstrate that the unfolding pathways are determined jointly by relative exposure of polar and non-polar residues of a protein and the mode of molecular action of a solvent on that protein.

q-bio.BM↗

arXiv2014

Anomalous Power Law Decay in Solvation Dynamics of DNA: A Mode Coupling Theory Analysis of Ion Contribution

Several time domain fluorescence Stokes shift (TDFSS) experiments have reported a slow power law decay in the hydration dynamics of a DNA molecule. Such a power law has neither been observed in computer simulations nor in some other TDFSS experiments. Here we observe that a slow decay may originate from collective ion contribution because in experiments DNA is immersed in a buffer solution, and also from groove bound water and lastly from DNA dynamics itself. In this work we first express the solvation time correlation function in terms of dynamic structure factors of the solution. We use mode coupling theory to calculate analytically the time dependence of collective ionic contribution. A power law decay in seen to originate from an interplay between long range probe-ion direct correlation function and ion-ion dynamic structure factor. Although the power law decay is reminiscent of Debye-Falkenhagen effect yet solvation dynamics is dominated by ion atmosphere relaxation times at longer length scales (small wave number) than in electrolyte friction. We further discuss why this power law may not originate from water motions which have been computed by molecular dynamics simulations. Lastly, we propose several experiments to check the prediction of the present theoretical work.

cond-mat.soft↗

arXiv2014

Melting/freezing transition in polydisperse Lennard-Jones system: Remarkable agreement between predictions of inherent structure, bifurcation phase diagram, Hansen-Verlet rule and Lindemann criteria

We use polydispersity in size as a control parameter to explore certain aspects of melting and freezing transitions in a system of Lennard-Jones spheres. Both analytical theory and computer simulations are employed to establish a potentially interesting relationship between observed terminal polydispersity in Lennard-Jones polydisperse spheres and prediction of the same in the integral equation based theoretical analysis of liquid-solid transition. As we increase polydispersity, solid becomes inherently unstable because of the strain built up due to the size disparity. This aspect is studied here by calculating the inherent structure (IS) calculation. With polydispersity at constant volume fraction we find initially a sharp rise of the average IS energy of the crystalline solid until transition polydispersity, followed by a cross over to a weaker dependence of IS energy on polydispersity in the amorphous state. This cross over from FCC to amorphous state predicted by IS analysis agrees remarkably well with the solid-liquid phase diagram (with extension into the metastable phase) generated by non-linear integral equation theories of freezing. Two other well-known criteria of freezing/melting transitions, the Hansen-Verlet rule of freezing and the Lindemann criterion of melting are both shown to be remarkably in good agreement with the above two estimates. Together they seem to indicate a small range of metastability in the liquid-solid transition in polydisperse solids.

cond-mat.soft↗

arXiv2014

Fluctuating micro-heterogeneity in water - tert-butyl alcohol mixtures and lambda-type divergence of the mean cluster size with phase transition-like multiple anomalies

Water - tert-butyl alcohol (TBA) binary mixture exhibits a large number of thermodynamic and dynamic anomalies. These anomalies are observed at surprisingly low TBA mole fraction, with $x_{\text{TBA}} \approx 0.03 - 0.07$. We demonstrate here that the origin of the anomalies lies in the local structural changes that occur due to self-aggregation of TBA molecules. We observe a percolation transition of the TBA molecules at $x_{\text{TBA}} \approx 0.05$. We note that "islands" of TBA clusters form even below this mole fraction, while a large spanning cluster emerges above that mole fraction. At this percolation threshold, we observe a lambda-type divergence in the fluctuation of the size of the largest TBA cluster, reminiscent of a critical point. Alongside, the structure of water is also perturbed, albeit weakly, by the aggregation of TBA molecules. There is a monotonic decrease in the tetrahedral order parameter of water, while the dipole moment correlation shows a weak non-linearity. Interestingly, water molecules themselves exhibit a reverse percolation transition at higher TBA concentration, $x_{\text{TBA}} \approx 0.45$, where large spanning water clusters now break-up into small clusters. This is accompanied by significant divergence of the fluctuations in the size of largest water cluster. This second transition gives rise to another set of anomalies around. Both the percolation transitions can be regarded as manifestations of Janus effect at small molecular level.

cond-mat.soft↗

arXiv2014

Correlation between thermodynamic anomalies and pathways of ice nucleation in supercooled water

The well-known classical nucleation theory (CNT) for the free energy barrier towards formation of a nucleus of critical size of the new stable phase within the parent metastable phase fails to take into account the influence of other metastable phases having density/order intermediate between the parent metastable phase and the final stable phase. This lacuna can be more serious than capillary approximation or spherical shape assumption made in CNT. This issue is particularly significant in ice nucleation because liquid water shows rich phase diagram consisting of two (high and low density) liquid phases in supercooled state. The explanations of thermodynamic and dynamic anomalies of supercooled water often invoke the possible influence of a liquid-liquid transition between two metastable liquid phases. To investigate both the role of thermodynamic anomalies and presence of distinct metastable liquid phases in supercooled water on ice nucleation, we employ density functional theoretical approach to find nucleation free energy barrier in different regions of phase diagram. The theory makes a number of striking predictions, such as a dramatic lowering of nucleation barrier due to presence of a metastable intermediate phase and crossover in the dependence of free energy barrier on temperature near liquid-liquid critical point. These predictions can be tested by computer simulations as well as by controlled experiments.

cond-mat.stat-mech↗

arXiv2013

Solvent Sensitivity of Protein Unfolding: Study of Chicken Villin Headpiece Subdomain in Water-Ethanol and Water-DMSO Mixtures

In the present work we study and compare unfolding of a small protein, chicken villin headpiece (HP-36) in two different aqueous binary mixtures, namely water-ethanol (EtOH) and water-dimethyl sulphoxide (DMSO). In both the binary mixtures, HP-36 is found to unfold (fully or partially, depending on the mixture) under ambient conditions, that otherwise requires temperature as high as ~600 K to denature in pure aqueous solvent. In all the cases, first step of unfolding is found to be similar, i.e. separation of the cluster formed by three hydrophobic (phenylalanine) residues, namely Phe-7, Phe-11 and Phe-18, which constitute the hydrophobic core, thereby initiating melting of helix-2 of the protein. Subsequent unfolding steps follow different paths in different chemical environments. As both water-DMSO and water-ethanol show composition dependent anomalies, so do the details of unfolding dynamics. With an increase of co-solvent concentration different partially unfolded intermediates are found to be formed in both the cases. This is reflected in a remarkable non-monotonic composition dependence of several order parameters, including fraction of native contacts and protein-solvent interaction energy. The emergence of such partially unfolded states is particularly attributed to the preferential solvation of the hydrophobic residues by the ethyl groups of ethanol and methyl groups of DMSO. While in DMSO the protein gradually attains a completely unfolded state at xDMSO=0.30, unfolding in water-ethanol appears to be more complex and sensitive to solvent composition.

q-bio.BM↗

arXiv2013

Vitamin D sensitivity to the immune responses and autoimmunity: A chemical network model study

Although Vitamin D is believed to be involved in a large number of immune responses our understanding of these processes at cellular level remained at infancy. We develop and solve a coarse grained kinetic network model to quantify the effects of variation of vitamin D on human immunity. The system of equations accounts for known inter-relation between active and inactive vitamin D, antigen presenting cells, effector T cells, regulatory T cells and pathogen. Both time dependent and steady state solutions are obtained. The time dependent solution of the system of equations reveals that the immune response is rather strongly regulated in presence of vitamin D. We found quantitatively that lower than optimum levels of concentration of active vitamin D correspond to weak regulation where, once a pathogen/antigen enters the body, the nature of the immune response would be less regulatory and hence more aggressive, or inflammatory. The steady state solution of our model shows that vitamin D enhances the tolerance level of immune system, thereby increasing resistance to autoimmune diseases. Our model and accompanied numerical analyses reveal another important aspect of immunity: While extremely low levels of vitamin D could lead to increased risk of autoimmune responses, an overdose (toxic) level would give rise to too large a tolerant response, leading to the increased risk of tumors and cancerous cell growth.

q-bio.MN↗

arXiv2013

Solid-solid collapse transition in a two dimensional model molecular system

Solid-solid collapse transition in open framework structures is ubiquitous in nature. The real difficulty in understanding detailed microscopic aspects of such transitions in molecular systems arises from the interplay between different energy and length scales involved in molecular systems, often mediated through a solvent. In this work we employ Monte Carlo (MC) simulations to study the collapse transition in a model molecular system interacting via both isotropic as well as anisotropic interactions having different length and energy scales. The model we use is known as Mercedes-Benz (MB) which for a specific set of parameters sustains three solid phases: honeycomb, oblique and triangular. In order to study the temperature induced collapse transition, we start with a metastable honeycomb solid and induce transition by heating. High density oblique solid so formed has two characteristic length scales corresponding to isotropic and anisotropic parts of interaction potential. Contrary to the common believe and classical nucleation theory, interestingly, we find linear strip-like nucleating clusters having significantly different order and average coordination number than the bulk stable phase. In the early stage of growth, the cluster grows as linear strip followed by branched and ring-like strips. The geometry of growing cluster is a consequence of the delicate balance between two types of interactions which enables the dominance of stabilizing energy over the destabilizing surface energy. The nuclei of stable oblique phase are wetted by intermediate order particles which minimizes the surface free energy. We observe different pathways for pressure and temperature induced transitions.

cond-mat.soft↗

arXiv2013

Kinetic proofreading at single molecular level: Aminoacylation of tRNA^{Ile} and the role of water as an editor

Proofreading/editing in protein synthesis is essential for accurate translation of information from the genetic code. In this article we present a theoretical investigation of efficiency of a kinetic proofreading mechanism that employs hydrolysis of the wrong substrate as the discriminatory step in enzyme catalytic reactions. We consider aminoacylation of tRNA^{Ile} which is a crucial step in protein synthesis and for which experimental results are now available. We present an augmented kinetic scheme and then employ methods of stochastic simulation algorithm to obtain time dependent concentrations of different substances involved in the reaction and their rates of formation. We obtain the rates of product formation and ATP hydrolysis for both correct and wrong substrates (isoleucine and valine in our case), in single molecular enzyme as well as ensemble enzyme kinetics. The present theoretical scheme correctly reproduces (i) the amplitude of the discrimination factor in the overall rates between isoleucine and valine which is obtained as (1.8 \times 10^2).(4.33 \times 10^2) = 7.8 \times 10^4, (ii) the rates of ATP hydrolysis for both Ile and Val at different substrate concentrations in the aminoacylation of tRNA^{Ile}. The present study shows a non-michaelis type dependence of rate of reaction on tRNA^{Ile} concentration in case of valine. The editing in steady state is found to be independent of amino acid concentration. Interestingly, the computed ATP hydrolysis rate for valine at high substrate concentration is same as the rate of formation of Ile-tRNA^{Ile} whereas at intermediate substrate concentration the ATP hydrolysis rate is relatively low.

q-bio.BM↗

arXiv2013

Nucleation of a stable solid from melt in the presence of multiple metastable intermediate phases: Wetting, Ostwald step rule and vanishing polymorphs

In many systems, nucleation of a stable solid may occur in the presence of other (often more than one) metastable phases. These may be polymorphic solids or even liquid phases. In such cases, nucleation of the solid phase from the melt may be facilitated by the metastable phase because the latter can "wet" the interface between the parent and the daughter phases, even though there may be no signature of the existence of metastable phase in the thermodynamic properties of the parent liquid and the stable solid phase. Straightforward application of classical nucleation theory (CNT) is flawed here as it overestimates the nucleation barrier since surface tension is overestimated (by neglecting the metastable phases of intermediate order) while the thermodynamic free energy gap between daughter and parent phases remains unchanged. In this work we discuss a density functional theory (DFT) based statistical mechanical approach to explore and quantify such facilitation. We construct a simple order parameter dependent free energy surface that we then use in DFT to calculate (i) the order parameter profile, (ii) the overall nucleation free energy barrier and (iii) the surface tension between the parent liquid and the metastable solid and also parent liquid and stable solid phases. The theory indeed finds that the nucleation free energy barrier can decrease significantly in the presence of wetting. This approach can provide a microscopic explanation of Ostwald step rule and the well-known phenomenon of "disappearing polymorphs" that depends on temperature and other thermodynamic conditions. Theory reveals a diverse scenario for phase transformation kinetics some of which may be explored via modern nanoscopic synthetic methods.

cond-mat.mtrl-sci↗

arXiv2013

Frequency dependence of specific heat in supercooled liquid water and emergence of correlated dynamics

Molecular origin of the well-known specific heat anomaly in supercooled liquid water is investigated here by using extensive computer simulations and theoretical analyses. A rather sharp increase in the values of isobaric specific heat with lowering temperature and the weak temperature dependence of isochoric specific heat in the same range are reproduced in simulations. We calculated the spatiotemporal correlation among temperature fluctuations and examined the frequency dependent specific heat. The latter shows a rapid growth in the low frequency regime as temperature is cooled below 270 K. In order to understand the microscopic basis of this increase, we have performed a shell wise decomposition of contributions of distant molecules to the temperature fluctuations in a central molecule. This decomposition reveals the emergence, at low temperatures, of temporally slow, spatially long ranged large temperature fluctuations. The temperature fluctuation time correlation function (TFCF) can be fitted to a William-Watts stretched exponential form with the stretching parameter close to 0.6 at low temperatures, indicating highly non-exponential relaxation. Temperature dependence of the relaxation time of the correlation function can be fitted to Vogel-Fulcher-Tamermann expression which provides a quantitative measure of the fragility of the liquid. Interestingly, we find that the rapid growth in the relaxation time of TFCF with lowering temperature undergoes a sharp crossover from a markedly fragile state to a weakly fragile state around 220 K.

cond-mat.soft↗

arXiv2013

Strongly first order melting of a two dimensional molecular solid

Melting and freezing transitions in two dimensional systems are known to show highly unusual characteristics. Most of the earlier studies considered atomic systems; the melting behavior in two dimensional molecular solids is still largely unexplored. In order to understand the role of multiple energy and length scales present in molecular systems on nature of melting transition, here we report computer simulation studies of melting of a two dimensional Mercedes-Benz (MB) system. We find that the interplay between the strength of isotropic and anisotropic interactions can give rise to rich phase diagram. The computed solid-liquid phase diagram consists of isotropic liquid and two crystalline phases - honeycomb and oblique. In contradiction to the celebrated KTHNY theory, we observe strongly one step first order melting transitions for both the honeycomb and oblique solids. The defects in both solids and liquids near the transition are more complex compared to the atomic systems.

cond-mat.mtrl-sci↗

arXiv2012

Phase transition in magnetically coupled spins on a ring (SOR) model

We have considered a new type of 'XY' model where spins are placed on concentric ring with constant spin density in every ring. The spin executes continuous rotation under a modified Shore-Zwanzig Hamiltonian (J. Chem. Phys. 63, 5445 (1975)). We have performed Monte Carlo simulation using Glauber acceptance criteria. Computations of Binder's cumulant, specific heat and magnetic susceptibility all show presence of a finite temperature order-disorder phase transition in this spin system. The system size dependence of Binder's cumulant suggests the existence of a phase transition with a transition temperature of T* = 1.2. However, we have found no signature of the occurrence of vortex in our SOR model. The absence of hysteresis rules out the possibility of first order phase transition. We have found two "stable" states for T* = 0 phase. The perfectly ordered true ground state is obtained by gradual cooling of the system, while the other is obtained by starting the simulation with a random configuration at T* = 0. This second state has higher energy than the perfectly aligned ground state.

cond-mat.stat-mech↗

arXiv2011

Terminal polydispersity in the crystallization of polydisperse Lennard-Jones liquid

We find through computer simulations that the fractional volume change on freezing of polydisperse Lennard-Jones liquid decreases with increasing polydispersity and approaches zero near a terminal polydispersity of 0.11, independent of temperature. The transition however remains first order at terminal polydispersity. Average inherent structure (IS) energy of the crystalline phase increases nearly quadratically with polydispersity indices (δ) and marked by a crossover to nearly constant IS energy in the amorphous phase.

cond-mat.soft↗

arXiv2011

Dynamic control of catalysis within biological cells

We develop a theory of enzyme catalysis within biological cells where the substrate concentration [S](t) is time dependent, in contrast to the Michaelis-Menten theory that assumes a steady state. We find that the time varying concentration can combine, in a non-linear way, with the ruggedness of the free energy landscape of enzymes (discovered both in single molecule studies and in simulations) to provide a highly efficient switch (or, bifurcation) between two catalytically active states, at a critical substrate concentration. This allows a dynamic control of product synthesis in cell.

cond-mat.stat-mech↗

arXiv2010

Dynamic coupling between the LID and NMP domain motions in the catalytic conversion of ATP and AMP to ADP by adenylate kinase

The catalytic conversion of ATP and AMP to ADP by adenylate kinase (ADK) involves large amplitude, ligand induced domain motions, involving the opening and the closing of LID and NMP domains, during the repeated catalytic cycle. We discover and analyze an interesting dynamical coupling between the motions of the two domains during the opening, using large scale atomistic molecular dynamics trajectory analysis, covariance analysis and multi-dimensional free energy calculations with explicit water. Initially, the LID domain must open by a certain amount before the NMP domain can begin to open. Dynamical correlation map shows interesting cross-peak between LID and NMP domain which suggests the presence of correlated motion between them. This is also reflected in our calculated two dimensional free energy surface contour diagram which has an interesting elliptic shape, revealing a strong correlation between the opening of the LID domain and that of the NMP domain. Our free energy surface of the LID domain motion is rugged due to interaction with water and the signature of ruggedness is evident in the observed RMSD variation and its fluctuation time correlation functions. We develop a correlated dynamical disorder type theoretical model to explain the observed dynamic coupling between the motions of the two domains in ADK. Our model correctly reproduces several features of the cross-correlation observed in simulations.

cond-mat.stat-mech↗

arXiv2010

Interplay between the range of attractive potential and metastability in gas-liquid nucleation

We find an interesting interplay between the range of the attractive part of the interaction potential and the extent of metastability (as measured by supersaturation) in gas-liquid nucleation. We explore and exploit this interplay to obtain new insight into nucleation phenomena. Just like its dependence on supersaturation (S), the free energy barrier of nucleation is found to depend strongly on the range of the interaction potential. Actually, the entire free energy surface, F(n), where n is the size of the liquid-like cluster, shows this dependence. The evidences and the reasons for this strong dependence are as follows. (i) The surface tension increases dramatically on increasing the range of interaction potential. In three dimensional Lennard-Jones system, the value of the surface tension increases from 0.494 for a cut-off of 2.5 σ to 1.09 when the full range of the potential is involved. In two dimensional LJ system, the value of the line tension increases from 0.05 to 0.18, under the same variation of the potential range. (ii) The density of the gas phase at coexistence decreases while that of the liquid phase increases substantially on increasing the range of the interaction potential. (iii) As a result of the above, at a given supersaturation S, the size of the critical nucleus and the free energy barrier both increase with increase in the range of interaction potential. (iv) Surprisingly, however, we find that the functional form predicted by the classical nucleation theory (CNT) for the dependence of the free energy barrier on the size of the nucleus to remain valid except at the largest value of S studied. (v) The agreement between CNT prediction and simulated values of the barrier is supersaturation dependent and worsens with increase in the range of interaction potential, and increases above 10 kBT at the largest supersaturation that could be studied.

cond-mat.stat-mech↗