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Debaprasad Giri

Publications and source records attributed to Debaprasad Giri.

15 recordsLinked to original sources

Adaptive dynamics of Ising spins in one dimension leveraging Reinforcement Learning

A one-dimensional flocking model using active Ising spins is studied, where the system evolves through the reinforcement learning approach \textit{via} defining state, action, and cost function for each spin. The orientation of spin with respect to its neighbouring spins defines its state. The state of spin is updated by altering its spin orientation in accordance with the $\varepsilon$-greedy algorithm (action) and selecting a finite step from a uniform distribution to update position. The $\varepsilon$ parameter is analogous to the thermal noise in the system. The cost function addresses cohesion among the spins. By exploring the system in the plane of the self-propulsion speed and $\varepsilon$ parameter, four distinct phases are found: disorder, flocking, flipping, and oscillatory. In the flipping phase, a condensed flock reverses its direction of motion stochastically. The mean reversal time $\langle T \rangle $ exponentially decays with $\varepsilon$. A new phase, an oscillatory phase, is also found, which is a chaotic phase with a positive Lyapunov exponent. The findings obtained from the reinforcement learning approach for the active Ising model system exhibit similarities with the outcomes of other conventional techniques, even without defining any explicit interaction among the spins.

cond-mat.soft

Effect of polydispersity on the dynamics of active Brownian particles

We numerically study the dynamics and the phases of self-propelled disk-shaped particles of different sizes with soft repulsive potential in two dimensions. Size diversity is introduced by the polydispersity index (PDI) $ε$, which is the width of the uniform distribution of the particle's radius. The self-propulsion speed of the particles controls the activity $v$. We observe enhanced dynamics for large size diversity among the particles. We calculate the effective diffusion coefficient $D_{eff}$ in the steady-state. The system exhibits four distinct phases, jammed phase with small $D_{eff}$ for small activity and liquid phase with enhanced $D_{eff}$ for large activity. The number fluctuation is larger and smaller than the equilibrium limit in the liquid and jammed phase, respectively. Further, the jammed phase is of two types: solid-jammed and liquid jammed for small and large PDI. Whereas the liquid phase is called motility induced phase separation (MIPS)-liquid for small PDI and for large PDI, we find enhanced diffusivity and call it the {\em pure liquid} phase. The system is studied for three packing densities $ϕ$, and the response of the system for polydispersity is the same for all $ϕ$'s. Our study can help understand the behavior of cells of various sizes in a tissue, artificial self-driven granular particles, or living organisms of different sizes in a dense environment.

cond-mat.soft

Statistical mechanics of a polymer chain attached to the interface of a cone-shaped channel

A polymer chain confined in nano-scale geometry has been used to investigate the underlying mechanism of Nuclear Pore Complex (NPC), where transport of cargoes is directional. It was shown here that depending on the solvent quality (good or poor) across the channel, a polymer chain can be either inside or outside the channel or both. Exact results based on the short chain revealed that a slight variation in the solvent quality can drag polymer chain inside the pore and {\it vice versa} similar to one seen in NPC. Furthermore, we also report the absence of crystalline (highly dense) state when the pore-size is less than the certain value, which may have potential application in packaging of DNA inside the preformed viral proheads.

cond-mat.soft

Scaling of hysteresis loop of interacting polymers under a periodic force

Using Langevin Dynamics simulations, we study a simple model of interacting-polymer under a periodic force. The force-extension curve strongly depends on the magnitude of the amplitude $(F)$ and the frequency ($ν$) of the applied force. In low frequency limit, the system retraces the thermodynamic path. At higher frequencies, response time is greater than the external time scale for change of force, which restrict the biomolecule to explore a smaller region of phase space that results in hysteresis of different shapes and sizes. We show the existence of dynamical transition, where area of hysteresis loop approaches to a large value from nearly zero area with decreasing frequency. The area of hysteresis loop is found to scale as $F^α ν^β$ for the fixed length. These exponents are found to be the same as of the mean field values for a time dependent hysteretic response to periodic force in case of the isotropic spin.

cond-mat.soft

Force induced unfolding of bio-polymers in a cellular environment: A model study

Effect of molecular crowding and confinement experienced by protein in the cell during unfolding has been studied by modeling a linear polymer chain on a percolation cluster. It is known that internal structure of the cell changes in time, however, they do not change significantly from their initial structure. In order to model this we introduce the correlation among the different disorder realizations. It was shown that the force-extension behavior for correlated disorder in both constant force ensemble (CFE) and constant distance ensemble (CDE) is significantly different than the one obtained in absence of molecular crowding.

cond-mat.soft

Stretching of a single-stranded DNA: Evidence for structural transition

Recent experiments have shown that the force-extension (F-x) curve for single-stranded DNA (ssDNA) consisting only of adenine [poly(dA)] is significantly different from thymine [poly(dT)]. Here, we show that the base stacking interaction is not sufficient to describe the F-x curves as seen in the experiments. A reduction in the reaction co-ordinate arising from the formation of helix at low forces and an increase in the distance between consecutive phosphates of unstacked bases in the stretched state at high force in the proposed model, qualitatively reproduces the experimentally observed features. The multi-step plateau in the F-x curve is a signature of structural change in ssDNA.

cond-mat.soft

Effects of Molecular Crowding on stretching of polymers in poor solvent

We consider a linear polymer chain in a disordered environment modeled by percolation clusters on a square lattice. The disordered environment is meant to roughly represent molecular crowding as seen in cells. The model may be viewed as the simplest representation of biopolymers in a cell. We show the existence of intermediate states during stretching arising as a consequence of molecular crowding. In the constant distance ensemble the force-extension curves exhibit oscillations. We observe the emergence of two or more peaks in the probability distribution curves signaling the coexistence of different states and indicating that the transition is discontinuous unlike what is observed in the absence of molecular crowding.

cond-mat.stat-mech

Force induced conformational transition in a system of interacting stiff polymer: Application to unfolding

We consider a stiff polymer chain in poor solvent and apply a force at one end of the chain. We find that by varying the stiffness parameter, polymer undergoes a transition from the globule state to the folded like state. The conformation of folded state mimics the $β$-sheet as seen in titin molecule. Using exact enumeration technique, we study the extension-force and force-temperature diagrams of such a system. Force-temperature diagram shows the re-entrance behaviour for flexible chain. However, for stiff chain this re-entrance behaviour is absent and there is an enhancement in $θ$-temperature with the rise of stiffness. We further propose that the internal information about the frozen structure of polymer can be read from the distribution of end-to-end distance which shows saw-tooth like behaviour.

cond-mat.soft

Effects of Eye-phase in DNA unzipping

The onset of an "eye-phase" and its role during the DNA unzipping is studied when a force is applied to the interior of the chain. The directionality of the hydrogen bond introduced here shows oscillations in force-extension curve similar to a "saw-tooth" kind of oscillations seen in the protein unfolding experiments. The effects of intermediates (hairpins) and stacking energies on the melting profile have also been discussed.

cond-mat.soft

Does changing the pulling direction give better insight into biomolecules?

Single molecule manipulation techniques reveal that the mechanical resistance of a protein depends on the direction of the applied force. Using a lattice model of polymers, we show that changing the pulling direction leads to different phase diagrams. The simple model proposed here indicates that in one case the system undergoes a transition akin to the unzipping of a $β$ sheet, while in the other case the transition is of a shearing (slippage) nature. Our results are qualitatively similar to experimental results. This demonstrates the importance of varying the pulling direction since this may yield enhanced insights into the molecular interactions responsible for the stability of biomolecules.

cond-mat.stat-mech

Statistical mechanics of coil-hairpin transition in a single stranded DNA oligomer

A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behavior of a short RNA or a single stranded DNA molecule that forms hairpin structure and calculate the properties associated with coil-hairpin transition by enumerating all possible conformations of a chain of N monomers in two and three dimensions. The first and last five monomers of the chain have been allowed to pair and form the stem of the hairpin structure while the remaining monomers can form a loop. The coil-hairpin transition is found to be first order with large entropy change. While the rate of unzipping of the hairpin stem is found to be independent of the length of the loop and the dimensionality of the space, the rate of closing varies greatly with loop length and dimensionality of the space.

cond-mat.stat-mech

Force induced triple point for interacting polymers

We show the existence of a force induced triple point in an interacting polymer problem that allows two zero-force thermal phase transitions. The phase diagrams for three different models of mutually attracting but self avoiding polymers are presented. One of these models has an intermediate phase and it shows a triple point but not the others. A general phase diagram with multicritical points in an extended parameter space is also discussed.

cond-mat.stat-mech

A simple model for the relative stabilities of DNA hairpin structure

A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behaviour of a single stranded short DNA molecule that form hairpin structure. Using exact enumeration method we calculate the properties associated with coil-hairpin transition. Our results are in qualitative agreement with the experiment.

cond-mat.soft

The Adsorption and Collapse Transitions in a Linear Polymer Chain near an Attractive Wall

We deduce the qualitative phase diagram of a long flexible neutral polymer chain immersed in a poor solvent near an attracting surface using phenomenological arguments. The actual positions of the phase boundaries are estimated numerically from series expansion up to 19 sites of a self-attracting self avoiding walk in three dimensions. In two dimensions, we calculate analytically phase boundaries in some cases for a partially directed model. Both the numerical as well as analytical results corroborate the proposed qualitative phase diagram.

cond-mat.stat-mech

Adsorbed states of a long - flexible polymer chain

A phase diagram for a surface-interacting long flexible polymer chain in a two-dimensional poor solvent where the possibility of collapse exists is determined using exact enumeration method. A model of a self-attracting self avoiding walk (SASAW) on a square lattice was considered and up to 28 steps in series were evaluated. A new adsorbed state having the conformation of a surface attached globule is found. Four phases (i) desorbed expanded, (ii) desorbed collapsed, (iii) adsorbed expanded and (iv) surface attached globule are found to meet at a point on the adsorption line.

cond-mat.stat-mech