arXiv subjects

Rajarshi Chakrabarti

Publications and source records attributed to Rajarshi Chakrabarti.

At least 37 records · Page 2Linked to original sources

arXiv2020

Escape of a passive particle from activity-induced energy landscape: Emergence of slow and fast effective diffusion

Spontaneous persistent motions driven by active processes play a central role to maintain the living cells far from equilibrium. In the majority of the research works, the steady state dynamics of an active system has been described in terms of an effective temperature. In the majority of the research works, the steady state dynamics of an active system has been described in terms of an effective temperature. By contrast, we have examined a prototype model for diffusion in an activity-induced rugged energy landscape to describe the slow dynamics of a tagged particle in a dense active environment. The expression for the mean escape time from the active rugged energy landscape holds only in the limit of low activity and the mean escape time from the rugged energy landscape increases with activity. The precise form of the active correlation will determine whether the mean escape time will depend on the persistence time or not. The active rugged energy landscape approach also allows an estimate of non-equilibrium effective diffusivity characterizing the slow diffusive motion of the tagged particle due to activity. On the other hand, in a dilute environment, high activity augments the diffusion of the tagged particle. The enhanced diffusion can be attributed to an effective temperature, higher than the ambient temperature and is used to calculate the Kramers' mean escape time, which decreases with activity. Our results have direct relevance to recent experiments on tagged particle diffusion in condensed phases.

cond-mat.stat-mech↗

arXiv2020

Wet and dry internal friction can be measured with the Jarzynski equality

The existence of two types of internal friction wet and dry is revisited, and a simple protocol is proposed for distinguishing between the two types and extracting the appropriate internal friction coefficient. The scheme requires repeatedly stretching a polymer molecule, and measuring the average work dissipated in the process by applying the Jarzynski equality. The internal friction coefficient is then estimated from the average dissipated work in the extrapolated limit of zero solvent viscosity. The validity of the protocol is established through analytical calculations on a one-dimensional free-draining Hookean spring-dashpot model for a polymer, and Brownian dynamics simulations of: (a) a single-mode nonlinear spring-dashpot model for a polymer, and (b) a finitely extensible bead-spring chain with cohesive intra-chain interactions, both of which incorporate fluctuating hydrodynamic interactions. Well-established single-molecule manipulation techniques, such as optical tweezer-based pulling, can be used to implement the suggested protocol experimentally.

cond-mat.soft↗

arXiv2019

Choline chloride as a nano-crowder protects HP-36 from urea-induced denaturation: Insights from Solvent Dynamics and Protein-Solvent interaction

Urea at sufficiently high concentration unfolds the secondary structure of proteins leading to denaturation. In contrast, Choline Chloride (ChCl) and urea, in 1:2 molar ratio form a deep eutectic mixture, a liquid at room temperature and protect proteins from denaturation. In order to get a microscopic picture of this phenomenon, we perform extensive all-atom molecular dynamics simulations on a model protein HP-36. Based on our calculation of Kirkwood-Buff integrals, we analyze the relative accumulation of these osmolytes around the protein. Additional insights are drawn from the analyses of the translational and rotational dynamics of solvent molecules and also from the hydrogen bond auto-correlation functions. In the presence of urea, water shows slow subdiffusive dynamics around the protein backbone as a consequence of stronger interaction of water molecules with the backbone atoms. Urea also shows subdiffusive motion. Addition of choline further slows down the dynamics of urea restricting its inclusion around the protein backbone. Adding to this, choline molecules in the first solvation shell of the protein shows the strongest subdiffusive behavior. In other words, ChCl behaves as a nano-crowder by excluding urea from the protein backbone and thereby slowing down the dynamics of the water layer around the protein. This prevents the protein from denaturation and makes it structurally rigid which in turn is supported by the smaller radius of gyration and root mean square deviation values of HP-36 when ChCl is present in the system.

cond-mat.soft↗

arXiv2019

Transport of probe particles in polymer network: effects of probe size, network rigidity and probe-polymer interaction

Fundamental understanding of the effect of microscopic parameters on the dynamics of probe particles in different complex environments has wide implications. Examples include diffusion of proteins in the biological hydrogels, porous media, polymer matrix, etc. Here, we use extensive molecular dynamics simulations to investigate the dynamics of the probe particle in a polymer network on a diamond lattice which provides substantial crowding to mimic the cellular environment. Our simulations show that the dynamics of the probe increasingly becomes restricted, non-Gaussian and subdiffusive on increasing the network rigidity, binding affinity and the probe size. In addition, the velocity autocorrelation functions show negative dips owing to the viscoelasticity and caging due to surrounding network. These observations go with general experimental findings. Surprisingly for a probe particle of size comparable to the mesh size, unrestricted motion engulfing large length scales has been observed. This happens with the more flexible polymer network, which is easily pushed by the bigger probe. Our study gives a general qualitative picture of transport of probes in gel like medium, as encountered in different contexts.

cond-mat.soft↗

arXiv2019

Effects of active fluctuations on energetics of a colloidal particle: superdiffusion, dissipation and entropy production

We consider a colloidal particle immersed in an active bath and derive a Smoluchowski equation that governs the dynamics of colloidal particle. We address this as active Smoluchowski equation. Our analysis based on this active Smoluchowski equation shows a short time superdiffusive behavior that strongly depends on the activity. Our model also predicts a non-monotonic dependence of mean energy dissipation against time, a signature of activity-induced dynamics. By introducing a frequency-dependent effective temperature, we show that the mean rate of entropy production is time dependent unlike a thermal system. The prime reason for these anomalies is the absence of any fluctuation-dissipation theorem for the active noise. We also comment on how microscopic details of activity can reverse the trends for mean energy dissipation and mean rate of entropy production.

cond-mat.stat-mech↗

arXiv2018

Enhanced diffusion, swelling and slow reconfiguration of a single chain in non-Gaussian active bath

A prime example of non-equilibrium or active environment is a biological cell. In order to understand in-vivo functioning of biomolecules such as proteins, chromatins, a description beyond equilibrium is absolutely necessary. In this context, biomolecules have been modeled as Rouse chains in Gaussian active bath. However, these non-equilibrium fluctuations in biological cells are non-Gaussian. This motivates us to take a Rouse chain subjected to a series of pulses of force with finite duration, mimicking run and tumble motion of a class of micro-organisms. Thus by construction, this active force is non-Gaussian. Our analytical calculations show that the mean square displacement (MSD) of center of mass (COM) grows faster and even shows superdiffusive behavior at higher activity, supporting recent experimental observation on active enzymes (A.-Y. Jee, Y.-K. Cho, S. Granick, and T. Tlusty, Proc. Natl. Acad. Sci. 115, 10812 (2018)), but chain reconfiguration is slower. The reconfiguration time of a chain with N monomers scales as N^sigma, where the exponent sigma=2. In addition, the chain swells. We compare this activity-induced swelling with that of a Rouse chain in a Gaussian active bath. In principle, our predictions can be verified by future single molecule experiments.

cond-mat.soft↗

arXiv2018

Rheological consequences of wet and dry friction in a dumbbell model with hydrodynamic interactions and internal viscosity

The effect of fluctuating internal viscosity and hydrodynamic interactions on a range of rheological properties of dilute polymer solutions is examined using a finitely extensible dumbbell model for a polymer. Brownian dynamics simulations are used to compute both transient and steady state viscometric functions in shear flow. The results enable a careful differentiation of the influence, on rheological properties, of solvent-mediated friction from that of a dissipative mechanism that is independent of solvent viscosity. In particular, hydrodynamic interactions have a significant influence on the magnitude of the stress jump at the inception of shear flow, and on the transient viscometric functions, but a negligible effect on the steady state viscometric functions at high shear rates. Zero-shear rate viscometric functions of free-draining dumbbells remain essentially independent of the internal viscosity parameter, as predicted by the Gaussian approximation, but the inclusion of hydrodynamic interactions induces a dependence on both the hydrodynamic interaction and the internal viscosity parameter. Large values of the internal viscosity parameter lead to linear viscoelastic predictions that mimic the behavior of rigid dumbbell solutions. On the other hand, steady-shear viscometric functions at high shear rates differ in general from those for rigid dumbbells, depending crucially on the finite extensibility of the dumbbell spring.

cond-mat.soft↗

arXiv2018

Entropy production and work fluctuation relations for a single particle in active bath

A colloidal particle immersed in a bath of bacteria is a typical example of a passive particle in an active bath. To model this, we take an overdamped harmonically trapped particle subjected to a thermal and a non-equilibrium noise arising from the active bath. The harmonic well can be attributed to a laser trap or to the small amplitude motion of the sedimented colloid at the bottom of the capillary. In the long time, the system reaches a non-equilibrium steady state that can be described by an effective temperature. By adopting this notion of effective temperature, we investigate whether fluctuation relations for entropy hold. In addition, when subjected to a deterministic time dependent drag, we find that transient fluctuation theorem for work cannot be applied in conventional form. However, a steady state fluctuation relation for work emerges out with a renormalized temperature.

cond-mat.stat-mech↗

arXiv2017

Diffusion of self-propelled Janus tracer in polymeric environment

Artificially synthesized Janus particles have tremendous prospective as in-vivo drug-delivery agents due to the possibility of self-propulsion by external stimuli. Here we report the first ever computational study of translational and rotational motion of self-propelled Janus tracers in a het- erogeneous polymeric environment. The presence of polymers makes the translational mean square displacement (MSD) of the Janus tracer to grow very slowly as compared to that of a free Janus tracer, but surprisingly the mean square angular displacement (MSAD) is significantly increased as observed in a recent experiment. Moreover, with the increasing propulsion velocity, MSAD grows even faster. However, when the repulsive polymers are replaced with polymers with sticky zones, MSD and MSAD both show sharp decline.

cond-mat.soft↗

arXiv2016

Tracer diffusion in a sea of polymers with binding zones: mobile vs frozen traps

We use molecular dynamics simulations to investigate the tracer diffusion in a sea of polymers with specific binding zones for the tracer. These binding zones act as traps. Our simulations show that the tracer can undergo normal yet non-Gaussian diffusion under certain circumstances, e.g, when the polymers with traps are frozen in space and the volume fraction and the binding strength of the traps are moderate. In this case, as the tracer moves, it experiences a heterogeneous environment and exhibits confined continuous time random walk (CTRW) like motion resulting a non-Gaussian behavior. Also the long time dynamics becomes subdiffusive as the number or the binding strength of the traps increases. However, if the polymers are mobile then the tracer dynamics is Gaussian but could be normal or subdiffusive depending on the number and the binding strength of the traps. In addition, with increasing binding strength and the number of the polymer traps, the probability of the tracer being trapped increases. On the other hand, removing the binding zones does not result trapping, even at comparatively high crowding. Our simulations also show that the trapping probability increases with the increasing size of the tracer and for a bigger tracer with the frozen polymer background the dynamics is only weakly non-Gaussian but highly subdiffusive. Our observations are in the same spirit as found in many recent experiments on tracer diffusion in polymeric materials and questions the validity of Gaussian theory to describe diffusion in crowded environment in general.

cond-mat.soft↗

arXiv2015

Chain reconfiguration in active noise

In a typical single molecule experiment, dynamics of an unfolded proteins is studied by determining the reconfiguration time using long-range Forster resonance energy transfer where the reconfiguration time is the characteristic decay time of the position correlation between two residues of the protein. In this paper we theoretically calculate the reconfiguration time for a single flexible polymer in presence of active noise. The study suggests that though the MSD grows faster, the chain reconfiguration is always slower in presence of long-lived active noise with exponential temporal correlation. Similar behavior is observed for a worm like semi-flexible chain and a Zimm chain. However it is primarily the characteristic correlation time of the active noise and not the strength that controls the increase in the reconfiguration time. In a nutshell, such active noise makes the polymer to move faster but the correlation loss between the monomers becomes slower.

cond-mat.soft↗

arXiv2015

Thermodynamics of site-specific small molecular ion interactions with DNA duplex: a molecular dynamics study

The stability and dynamics of a double-stranded DNA (dsDNA) is affected by the preferential occupancy of small monovalent molecular ions. Small metal and molecular ions such as sodium and alkyl ammonium have crucial biological functions in human body, affect the thermodynamic stability of the duplex DNA and exhibit preferential binding. Here, using atomistic molecular dynamics simulations we investigate the preferential binding of metal ion such as Na+ and molecular ions such as tetramethyl ammonium (TMA+) and 2-hydroxy-N,N,N-trimethylethanaminium (CHO+) to double stranded DNA. The thermodynamic driving force for a particular molecular ion- DNA interaction is determined by decomposing the free energy of binding into its entropic and enthalpic contributions. Our simulations show that each of these molecular ions preferentially binds to the minor groove of the DNA and the extent of binding is highest for CHO+. The ion binding processes are found to be entropically favourable. In addition, the contribution of hydrophobic effects towards the entropic stabilization (in case of TMA+) and the effect of hydrogen bonding contributing to enthalpic stabilization (in case of CHO+) have also been investigated.

cond-mat.soft↗

arXiv2015

Ion assisted structural collapse of a single stranded DNA: a molecular dynamics approach

The structure and dynamics of negatively charged nucleic acids strongly correlate with the concentration and charge of the oppositely charged counter-ions. It is well known that the structural collapse of DNA is favored in the presence of additional salt, a source of excess oppositely charged ions. Under such conditions single stranded DNA adopts a collapsed coil like conformation, typically characterized by stacking base pairs. Using atomistic molecular dynamics simulation, we demonstrate that in the presence of additional divalent salt (MgCl2) single stranded DNA (Dickerson Drew dodecamer) initially collapses and then expands with increasing salt concentration. This is due to the overcharging induced DNA chain swelling, a dominant factor at a higher divalent salt concentration. In a nutshell, our simulations show how in the presence of divalent salt, non-sequential base stacking and overcharging competes and affect single stranded DNA dynamics unlike a monovalent salt.

cond-mat.soft↗

arXiv2015

Reconfiguration Dynamics in folded and intrinsically disordered protein with internal friction: Effect of solvent quality and denaturant

We consider a phantom chain model of polymer with internal friction in a harmonic confinement and extend it to take care of effects of solvent quality following a mean field approach where an exponent $ν$ is introduced. The model termed as "Solvent Dependent Compacted Rouse with Internal Friction (SDCRIF)" is then used to calculate the reconfiguration time of a chain that relates to recent Förster resonance energy transfer (FRET) studies on folded and intrinsically disordered proteins (IDPs) and can account for the effects of solvent quality as well as the denaturant concentration on the reconfiguration dynamics. Following an ansatz that relates the strength of the harmonic confinement ($k_c$) with the internal friction of the chain ($ξ_{int}$), SDCRIF can convincingly reproduce the experimental data and explain how the denaturant can change the time scale for the internal friction. It can also predict near zero internal friction in case of IDPs. In addition, our calculations show that the looping time as well as the reconfiguration time scales with the chain length $N$ as $\sim N^α$, where $α$ depends weakly on the internal friction but has rather stronger dependence on the solvent quality. In absence of any internal friction, $α=2ν+1$ and it goes down in presence of internal friction, but looping slows down in general. On the contrary, poorer the solvent, faster the chain reconfigures and forms loop, even though one expects high internal friction in the collapsed state. However, if the internal friction is too high then the looping and reconfiguration dynamics become slow even in poor solvent.

cond-mat.soft↗

arXiv2015

Looping dynamics of flexible chain with internal friction at different degree of compactness

Recently single molecule experiments have shown the importance of internal friction in biopolymer dynamics. Such studies also suggested that the internal friction although independent of solvent viscosity has strong dependence on denaturant concentration. Recent simulations also support such propositions by pointing out weak interactions to be the origin of internal friction in proteins. Here we made an attempt to investigate how a single polymer chain with internal friction undergoes reconfiguration and looping dynamics in a confining potential which accounts for the presence of the denaturant, by using recently proposed Compacted Rouse with internal friction (CRIF). We also incorporated the effect of hydrodynamics by extending this further to Compacted Zimm with internal friction (CZIF). All the calculations are carried out within the Wilemski Fixmann (WF) framework. By changing the strength of the confinement we mimicked chains with different degrees of compactness at different denaturant concentrations. While compared with experiments our results are found to be in good agreement.

cond-mat.soft↗

arXiv2014

Looping and reconfiguration dynamics of a flexible chain with internal friction

In recent past, experiments and simulations have suggested that apart from the solvent friction, friction arising from the protein itself plays an important role in protein folding by affecting the intra-chain loop formation dynamics. This friction is termed as internal friction in the literature. Using a flexible Gaussian chain with internal friction we analyze the intra- chain reconfiguration and loop formation times for all three topology classes namely end-to- end, end-to-interior and interior-to-interior. In a nutshell, bypassing expensive simulations we show how simple models like that of Rouse and Zimm can support the single molecule experiment and computer simulation results on intra-chain diffusion coefficients, looping time and even can predict the effects of tail length on the looping time.

cond-mat.soft↗

arXiv2012

Investigation of tracer diffusion in crowded cylindrical channel

Based on a coarse-grained model, we carry out molecular dynamics simulations to analyze the diffusion of a small tracer particle inside a cylindrical channel whose inner wall is covered with randomly grafted short polymeric chains. We observe an interesting transient subdiffusive behavior along the cylindrical axis at high attraction between the tracer and the chains, however, the long time diffusion is always normal. This process is found to be enhanced for the case that we immobilize the grafted chains, i.e. the sub-diffusive behavior sets in at an earlier time and spans over a longer time period before becoming diffusive. Even if the grafted chains are replaced with a frozen sea of repulsive, non-connected particles in the background, the transient subdiffusion is observed. The intermediate subdiffusive behavior only disappears when the grafted chains are replaced with a mobile background sea of mutually repulsive particles. Overall, the long time diffusion coefficient of the tracer along the cylinder axis decreases with the increase in system volume fraction, strength of attraction between the tracer and the background and also on freezing the background. We believe that the simple model presented here could be useful for a qualitative understanding of the process of macromolecular diffusion inside the nuclear pore complex.

cond-mat.soft↗

arXiv2012

Dynamics of end to end loop formation for an isolated chain in viscoelastic fluid

We theoretically investigate the looping dynamics of a linear polymer immersed in a viscoelastic fluid. The dynamics of the chain is governed by a Rouse model with a fractional memory kernel recently proposed by Weber et al. (S. C. Weber, J. A. Theriot, and A. J. Spakowitz, Phys. Rev. E 82, 011913 (2010)). Using the Wilemski-Fixman (G. Wilemski and M. Fixman, J. Chem. Phys. 60, 866 (1974)) formalism we calculate the looping time for a chain in a viscoelastic fluid where the mean square displacement of the center of mass of the chain scales as t^(1/2). We observe that the looping time is faster for the chain in viscoelastic fluid than for a Rouse chain in Newtonian fluid up to a chain length and above this chain length the trend is reversed. Also no scaling of the looping time with the length of the chain seems to exist for the chain in viscoelastic fluid.

cond-mat.soft↗