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Author: search.filters.author.Dutta, Sandipan

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    Exploring the unfolding pathways of protein families using elastic network model
    (Springer Nature, 2024-10) Dutta, Sandipan
    We explore how a protein’s native structure determines its unfolding process. We examine how the local structural features, like shear, and the global structural properties, like the number of soft modes, change during unfolding. Simulations are performed using a Gaussian Network Model (GNM) with bond breaking for both thermal and force-induced unfolding scenarios. We find that unfolding starts in areas of high shear in the native structure and progressively spreads to the low shear regions. Interestingly, analysis of single domain protein families (Chymotrypsin inhibitor and Barnase) reveal that proteins with distinct unfolding pathways exhibit divergent behavior of the number of soft modes during unfolding. This suggests that the number of soft modes might be a valuable tool for understanding thermal unfolding pathways. Additionally, we found a strong link between a protein’s overall structural similarity (TM-score) and its unfolding pathways, highlighting the importance of the native structure in determining how a protein unfolds.
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    Hydration of ions in two-dimensional water
    (APS, 2015-10) Dutta, Sandipan
    We present a two-dimensional lattice model of water to study the effects of ion hydration on the properties of water. We map the water molecules as lattice particles consisting of a single oxygen atom at the center of a site and two hydrogen atoms on each side. The internal state of the system, such as the dipole moment at a site, is defined with respect to the location of the hydrogen atoms at the site depending on their role in hydrogen bonds (H bonds) being a donor or an acceptor. We study the influence of the charge and the radius of the ion on the insertion energy and on the H bonds in the first and second hydration layers around the ion and in the bulk. In particular we analyze how the competing interactions of the short-ranged H bonds and the long-ranged electrostatics influence the hydration properties. The role of the ion both as a source of the electrostatic interactions as well as a defect is also discussed. Our model also shows the well-known fact that the polarizability of the water molecules destroys the hydrogen bond network and increases the dipole moment of the molecules near the ion.
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    Entropy production in active Rouse polymers
    (IOP, 2023-03) Dutta, Sandipan
    Active polymers are the archetype of nonequilibrium viscoelastic systems that constantly consume energy to produce motion. The activity of many biopolymers is essential to many life processes. The entropy production rate quantifies their non-equilibrium nature through the breaking of the time reversal symmetry. In this work we build an analytical model of active polymers as active Rouse polymers where the beads are active OrnsteinUhlenbeck particles (AOUP) and calculate their entropy production. The interactions between the beads are decoupled through the normal mode analysis and the entropy production can be solved analytically. We obtain the contribution of each Rouse mode in the entropy production and the dependence of the entropy production on the polymer properties like length. We find that the entropy production is zero for a passive Rouse polymer in the presence of thermal bath as well as for an active Rouse polymer in the absence of thermal bath. For an active chain in the presence of a thermal bath the entropy production is non-zero. In this case we find that the local temporal entropy production dominates the non-local entropy production.
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    Most probable paths for active Ornstein-Uhlenbeck particles
    (APS, 2023-05) Dutta, Sandipan
    Fluctuations play an important role in the dynamics of stochastic systems. In particular, for small systems, the most probable thermodynamic quantities differ from their averages because of the fluctuations. Using the Onsager Machlup variational formalism we analyze the most probable paths for nonequilibrium systems, in particular, active Ornstein-Uhlenbeck particles, and investigate how the entropy production along these paths differs from the average entropy production. We investigate how much information about their nonequilibrium nature can be obtained from their extremum paths and how these paths depend on the persistence time and their swim velocities. We also look at how the entropy production along the most probable paths varies with the active noise and how it differs from the average entropy production. This study would be useful to design artificial active systems with certain target trajectories.
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    Thermodynamics of multiple Maxwell demons
    (Springer, 2022-08) Dutta, Sandipan
    In many assembly line processes like metabolic and signaling networks in biological systems, the products of the first enzyme are the reactant for the next enzyme in the network. Working of multiple machines leads to efficient utilization of resources. Motivated by this, we investigate if multiple Maxwell demons lead to more efficient information processing. We study the phase space of multiple demons acting on an information tape based on the model of Mandal and Jarzynski [1, 2]. Their model is analytically solvable and the phase space of the device has three regions: engine, where work is delivered by writing information to the tape, erasure, where work is performed on the device to erase information on the tape, and dud, when work is performed and, at the same time, the information is written to the tape. For identical demons, we find that the erasure region increases at the expense of the dud region, while the information engine region does not change appreciably. The efficiency of the multiple demon device increases with the number of demons in the device and saturates to the equilibrium (maximum) efficiency even at short cycle times for very large numbers of demons. By investigating a device with non-identical demons acting on a tape, we identify the demon parameters that control the different regions of the phase space. Our model is well suited to study information processing in assembly line systems.
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    Finite Temperature Quantum Effects in Many-Body Systems by Classical Methods
    (Elsevier, 2016) Dutta, Sandipan
    A recent description of an exact map for the equilibrium structure and thermodynamics of a quantum system onto a corresponding classical system is summarized. Approximate implementations are constructed by pinning exact limits (ideal gas, weak coupling) and illustrated by calculation of pair correlations for the uniform electron gas and shell structure for harmonically confined charges. A wide range of temperatures and densities are addressed in each case. For the electron gas, comparisons are made to recent path integral Monte Carlo simulations showing good agreement. Finally, the relevance for orbital-free density functional theory for conditions of warm, dense matter is discussed briefly.
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    Shell formation in short like-charged polyelectrolytes in a harmonic trap
    (APS, 2016-01) Dutta, Sandipan
    Inspired by recent experiments and simulations on pattern formation in biomolecules by optical tweezers, a theoretical description based on the reference interaction site model (RISM) is developed to calculate the equilibrium density profiles of small polyelectrolytes in an external potential. The formalism is applied to the specific case of a finite number of Gaussian and rodlike polyelectrolytes trapped in a harmonic potential. The density profiles of the polyelectrolytes are studied over a range of lengths and numbers of polyelectrolytes in the trap, and the strength of the trap potential. For smaller polymers we recover the results for point charges. In the mean field limit the longer polymers, unlike point charges, form a shell at the boundary layer. When the interpolymer correlations are included, the density profiles of the polymers show sharp shells even at weaker trap strengths. The implications of these results are discussed.
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    Adsorption of highly charged Gaussian polyelectrolytes onto oppositely charged surfaces
    (AIP, 2016-03) Dutta, Sandipan
    In many biological processes highly charged biopolymers are adsorbed onto oppositely charged surfaces of macroions and membranes. They form strongly correlated structures close to the surface which cannot be explained by the conventional Poisson-Boltzmann theory. In this work strong coupling theory is used to study the adsorption of highly charged Gaussian polyelectrolytes. Two cases of adsorptions are considered, when the Gaussian polyelectrolytes are confined (a) by one charged wall, and (b) between two charged walls. The effects of salt and the geometry of the polymers on their adsorption-depletion transitions in the strong coupling regime are discussed.
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    Entangled polymer complexes as Higgs phenomena
    (RSC, 2015-08) Dutta, Sandipan
    We derive an effective Maxwell–London equation for entangled polymer complexes under topological constraints, borrowing the theoretical framework from topological field theory. We find that the transverse current flux of a test polymer chain, surrounded by entangled chains, decays exponentially from its centerline position with a finite penetration depth, which is analogous to the magnetic-field decay in a superconductor (SC), referred to as the Meissner effect. Just as the mass acquirement of photons in a SC is the origin of the magnetic-field decay, the polymer obtains uncrossable intersections along the chain due to the preservation of the linking number, which restricts the deviation of the transverse polymer current in the normal direction. The underlying physics is as follows: less flexible polymers have stronger current–current correlations, giving rise to a heavier effective mass of the gauge fields and resulting in a shorter decay length. Interestingly, this picture is well incorporated within the most successful phenomenological theory of the, so called, tube model, the microscopic origins of which researchers have long pursued. The correspondence of our equation of motion to the tube model claims that the confining tube potential is a consequence of the topological constraint (linking number). The tube radius is attributed to the decay length. On increasing the effective mass (by strengthening the interaction at an uncrossable intersection or a number of intersections), the tube becomes narrower. Using this argument, the exponential decay of the chain leakage out of the tube is well understood.
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    Finite-temperature quantum effects on confined charges
    (APS, 2016-11) Dutta, Sandipan
    A quantum system of N Coulomb charges confined within a harmonic trap is considered over a wide range of densities and temperatures. A recently described construction of an equivalent classical system is applied in order to exploit the rather complete classical description of harmonic confinement via liquid-state theory. Here, the effects of quantum mechanics on that representation are described with attention focused on the origin and nature of shell structure. The analysis extends from the classical strong Coulomb coupling conditions of dusty plasmas to the opposite limit of low temperatures and large densities characteristic of “warm, dense matter.”