Related papers: Allostery and Kinetic Proofreading
Robotic cell injection is used for automatically delivering substances into a cell and is an integral component of drug development, genetic engineering and many other areas of cell biology. Traditionally, the correctness of functionality…
The composite cytoskeleton, comprising interacting networks of semiflexible actin and rigid microtubules, actively generates forces and restructures using motor proteins such as myosins to enable key mechanical processes including cell…
Allosteric interactions in DNA are crucial for various biological processes. These interactions are quantified by measuring the change in free energy as a function of the distance between the binding sites for two ligands. Here we show that…
The standard two-step model of homogeneous-catalyzed reactions had been theoretically analyzed at various levels of approximations from time to time. The primary aim was to check the validity of the quasi-steady-state approximation, and…
Catalysis, the acceleration of chemical reactions by molecules that are not consumed in the process, is essential to living organisms but currently absent in physical systems that aspire to emulate biological functionalities with artificial…
Non-stoquastic drivers are known to improve the performance of quantum annealing by reducing first-order phase transitions into second-order ones in several mean-field-type model systems. Nevertheless, statistical-mechanical analysis shows…
Proteins are the workhorse molecules of the cell and perform their biological functions by binding to other molecules through physical contact. Protein function is then regulated through coupling of bindings on the protein (allosteric…
Recent quantum algorithms pertaining to electronic structure theory primarily focus on threshold-based dynamic construction of ansatz by selectively including important many-body operators. These methods can be made systematically more…
Humans prove theorems by relying on substantial high-level reasoning and problem-specific insights. Proof assistants offer a formalism that resembles human mathematical reasoning, representing theorems in higher-order logic and proofs as…
In recent literature there has been a lot of interest in the phenomena of noise induced transport in the absence of an average bias occurring in spatially periodic systems far from equilibrium. One of the main motivations in this area is to…
The levels of agility and flight or swimming performance demonstrated by insects, birds, fish, and even some aquatic invertebrates, are often vastly superior to what even the most advanced human-engineered vehicles operating in the same…
Accurate prediction of binding free energies is critical to streamlining the drug development and protein design process. With the advent of GPU acceleration, absolute alchemical methods, which simulate the removal of ligand electrostatics…
A recent paper by Gislason published in Am. J. Phys. deals with the celebrated example of the so-called "adiabatic piston", a system involving two ideal gases contained in a horizontal cylinder and separated by an insulating piston that…
In this work we study the assisted translocation of a polymer across a membrane nanopore, inside which a molecular motor exerts a force fuelled by the hydrolysis of ATP molecules. In our model the motor switches to its active state for a…
Elastic network models (ENM) and constraint-based, topological rigidity analysis are two distinct, coarse-grained approaches to study conformational flexibility of macromolecules. In the two decades since their introduction, both have…
The nonlinearity of dynamics in systems biology makes it hard to infer them from experimental data. Simple linear models are computationally efficient, but cannot incorporate these important nonlinearities. An adaptive method based on the…
Odd viscosity arises in systems with time reversal symmetry breaking, which creates non-dissipative effects. One method to probe changes in viscosity is to examine the dynamics of a single probe particle driven though a medium, a technique…
The precise details of how myosin-V coordinates the biochemical reactions and mechanical motions of its two head elements to engineer effective processive molecular motion along actin filaments remain unresolved. We compare a quantitative…
Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions are dominated by solvation and electrostatic energies and modulated by protein…
Living systems efficiently use chemical fuel to do work, process information, and assemble patterns despite thermal noise. Whether high efficiency arises from general principles or specific fine-tuning is unknown. Here, applying a recent…