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Molecular dynamics (MD) has become a powerful tool for studying biophysical systems, due to increasing computational power and availability of software. Although MD has made many contributions to better understanding these complex…
F1-ATPase catalyses ATP hydrolysis and converts the cellular chemical energy into mechanical rotation. The hydrolysis reaction in F1-ATPase does not follow the widely believed Michaelis-Menten mechanism. Instead, the hydrolysis mechanism…
In a stochastic heat engine driven by a cyclic non-equilibrium protocol, fluctuations in work and heat give rise to a fluctuating efficiency. Using computer simulations and tools from large deviation theory, we have examined these…
A robot can invoke heterogeneous computation resources such as CPUs, cloud GPU servers, or even human computation for achieving a high-level goal. The problem of invoking an appropriate computation model so that it will successfully…
The enzyme FoF1-ATP synthase provides the 'chemical energy currency' adenosine triphosphate (ATP) for living cells. Catalysis is driven by mechanochemical coupling of subunit rotation within the enzyme with conformational changes in the…
Motor proteins are active enzymatic molecules that drive a variety of biological processes, including transfer of genetic information, cellular transport, cell motility and muscles contraction. It is known that these biological molecular…
Multi-time-scale stochastic approximation is an iterative algorithm for finding the fixed point of a set of $N$ coupled operators given their noisy samples. It has been observed that due to the coupling between the decision variables and…
Cells control fluid flows with a spatial and temporal precision that far exceeds the capabilities of current microfluidic technologies. Cells achieve this superior spatio-temporal control by harnessing dynamic networks of cytoskeleton and…
Biological molecular machines are enzymes that simultaneously catalyze two processes, one donating free energy and second accepting it. Recent studies show that most native protein enzymes have a rich stochastic dynamics that often…
We present the stochastic thermodynamics analysis of an open quantum system weakly coupled to multiple reservoirs and driven by a rapidly oscillating external field. The analysis is built on a modified stochastic master equation in the…
In this paper, we derive a number of inequalities which express power-efficiency trade-offs that hold generally for thermodynamic machines operating in non-equilibrium stationary states. One of these inequalities concerns the output power,…
Single molecular rotor is an important component for constructing bot-tom-up molecular mechanical machines and a window for shedding light on complex physical and chemical questions about motions of organic molecules on surfaces. Stability…
Matter, especially DNA, is now programmed to carry out useful processes at the nanoscale. As these programs and processes become more complex and their envisioned safety-critical applications approach deployment, it is essential to develop…
We analyze a simple stochastic model to describe motor molecules which cooperate in large groups and present a physical mechanism which can lead to oscillatory motion if the motors are elastically coupled to their environment. Beyond a…
The discovery of functional molecules is an expensive and time-consuming process, exemplified by the rising costs of small molecule therapeutic discovery. One class of techniques of growing interest for early-stage drug discovery is de novo…
Malleable scheduling is a model that captures the possibility of parallelization to expedite the completion of time-critical tasks. A malleable job can be allocated and processed simultaneously on multiple machines, occupying the same time…
We analyze a steady-state thermoelectric engine, whose working substance consists of two capacitively coupled quantum dots. One dot is tunnel-coupled to a hot reservoir serving as a heat source, the other one to two electrically biased…
The effect of modifying substituents in the rotor group of five second generation molecular motors is estimated by theoretical calculations. The rotational speed is estimated by calculating the rate limiting step, the thermal helix…
Recent transportation research highlights the potential of autonomous vehicles (AV) to improve traffic flow mobility as they are able to maintain smaller car-following distances. However, as a unique class of ground robots, AVs are…
We present a novel approach to investigate the long-time stochastic dynamics of multi-dimensional classical systems, in contact with a heat-bath. When the potential energy landscape is rugged, the kinetics displays a decoupling of short and…