arXiv subjects

Shreyas Bhaban

Publications and source records attributed to Shreyas Bhaban.

7 recordsLinked to original sources

arXiv2023

Hindering loads prompt clustered configurations that enhance stability during cargo transport by multiple Kinesin-1

Transport of intracellular cargo is often mediated by teams of molecular motors that function in a chaotic environment under varying conditions. We show that the motors have unique steady state behavior which enables transport modalities that are robust. Under reduced ATP concentrations, multi-motor configurations are preferred over single motors. Higher load force drives motors to cluster, but very high loads compel them to separate in a manner that promotes immediate cargo movement once the load subsides. These inferences, backed by analytical guarantees, provide unique insights into the coordination strategies adopted by molecular motors to transport intracellular cargo.

q-bio.SC↗

arXiv2020

The Differential Entropy of Mixtures: New Bounds and Applications

Mixture distributions are extensively used as a modeling tool in diverse areas from machine learning to communications engineering to physics, and obtaining bounds on the entropy of probability distributions is of fundamental importance in many of these applications. This article provides sharp bounds on the entropy concavity deficit, which is the difference between the entropy of the mixture and the weighted sum of entropies of constituent components. Toward establishing lower and upper bounds on the concavity deficit, results that are of importance in their own right are obtained. In order to obtain nontrivial upper bounds, properties of the skew-divergence are developed and notions of "skew" $f$-divergences are introduced; a reverse Pinsker inequality and a bound on Jensen-Shannon divergence are obtained along the way. Complementary lower bounds are derived with special attention paid to the case that corresponds to independent summation of a continuous and a discrete random variable. Several applications of the bounds are delineated, including to mutual information of additive noise channels, thermodynamics of computation, and functional inequalities.

cs.IT↗

arXiv2018

Error Bounds on a Mixed Entropy Inequality

Motivated by the entropy computations relevant to the evaluation of decrease in entropy in bit reset operations, the authors investigate the deficit in an entropic inequality involving two independent random variables, one continuous and the other discrete. In the case where the continuous random variable is Gaussian, we derive strong quantitative bounds on the deficit in the inequality. More explicitly it is shown that the decay of the deficit is sub-Gaussian with respect to the reciprocal of the standard deviation of the Gaussian variable. What is more, up to rational terms these results are shown to be sharp.

cs.IT↗

arXiv2018

Designing Memory Bits with Dissipation lower than the Landauer's Bound

A Brownian particle in a symmetric double well potential is used as a representation for a single bit memory, where, the location of the particle in either well denotes one of the two states of a single bit memory. This article analyzes the effect of modifications to a symmetric double well potential on the minimum heat dissipation associated with erasure of the information stored in a single bit memory. Two types of modifications are considered, viz., overlap between the two wells and the asymmetry between the two wells of a bit of memory. Moreover, the analysis presented here, takes into account the uncertainty in the success of the erasure process. We quantify the effect of the proposed modifications on the heat dissipation accompanying erasure of a bit of information with a comparison to the Landauer's bound. In particular, we conclude that the proposed modifications could result in the minimum heat dissipation being lower than the Landauer's bound in quasi-static erasure processes. Furthermore, we quantify the physical aspect ratio for designing a memory bit which could improve memory density.

cond-mat.stat-mech↗

arXiv2017

Single Molecule Studies Under Constant Force Using Model Based Robust Control Design

Optical tweezers have enabled important insights into intracellular transport through the investigation of motor proteins, with their ability to manipulate particles at the microscale, affording femto Newton force resolution. Its use to realize a constant force clamp has enabled vital insights into the behavior of motor proteins under different load conditions. However, the varying nature of disturbances and the effect of thermal noise pose key challenges to force regulation. Furthermore, often the main aim of many studies is to determine the motion of the motor and the statistics related to the motion, which can be at odds with the force regulation objective. In this article, we propose a mixed objective H2-Hinfinity optimization framework using a model-based design, that achieves the dual goals of force regulation and real time motion estimation with quantifiable guarantees. Here, we minimize the Hinfinity norm for the force regulation and error in step estimation while maintaining the H2 norm of the noise on step estimate within user specified bounds. We demonstrate the efficacy of the framework through extensive simulations and an experimental implementation using an optical tweezer setup with live samples of the motor protein kinesin; where regulation of forces below 1 pico Newton with errors below 10 percent is obtained while simultaneously providing real time estimates of motor motion.

math.OC↗

arXiv2017

Memory Erasure using Time Multiplexed Potentials

We study the thermodynamics of a Brownian particle under the influence of a time multiplexed harmonic potential of finite width. The memory storage mechanism and the erasure protocol realized by time multiplexed potentials are utilized to experimentally realize erasure with work close to the Landauer's bound. We quantify the work done on the system with respect to the duty-ratio of time multiplexing, which also provides a handle to approach reversible erasures. A Langevin dynamics based simulation model is developed for the proposed memory bit and the erasure protocol, which guides the experimental realization. The study also provides insights into transport at the micro scale.

cond-mat.stat-mech↗

arXiv2016

Emergent Transport Properties of Molecular Motor Ensemble Affected by Single Motor Mutations

Intracellular transport is an essential function in eucaryotic cells, facilitated by motor proteins - proteins converting chemical energy into kinetic energy. It is known that motor proteins work in teams enabling unidirectional and bidirectional transport of intracellular cargo over long distances. Disruptions of the underlying transport mechanisms, often caused by mutations that alter single motor characteristics, are known to cause neurodegenerative diseases. For example, phosphorylation of kinesin motor domain at the serine residue is implicated in Huntington's disease, with a recent study of phosphorylated and phosphomimetic serine residues indicating lowered single motor stalling forces. In this article we report the effects of mutations of this nature on transport properties of cargo carried by multiple wild-type and mutant motors. Results indicate that mutants with altered stall forces might determine the average velocity and run-length even when they are outnumbered by wild type motors in the ensemble. It is shown that mutants gain a competitive advantage and lead to an increase in expected run-length when load on the cargo is in the vicinity of the mutant's stalling force or a multiple of its stalling force. A separate contribution of this article is the development of a semi-analytic method to analyze transport of cargo by multiple motors of multiple types. The technique determines transition rates between various relative configurations of motors carrying the cargo using the transition rates between various absolute configurations. This enables exact computation of average velocity and run-length. It can also be used to introduce alterations of various single motor parameters to model a mutation and to deduce effects of such alterations on the transport of a common cargo by multiple motors. Our method is easily implementable and we provide a software package for general use.

q-bio.SC↗