Related papers: RNA polymerase motors: dwell time distribution, ve…
This paper presents a molecular mechanics study for new nanorobotic structures using molecular dynamics (MD) simulations coupled to virtual reality (VR) techniques. The operator can design and characterize through molecular dynamics…
Biopolymer length regulation is a complex process that involves a large number of subprocesses acting simultaneously across multiple spatial and temporal scales. An illustrative example important for genomic stability is the length…
We introduce a model for translational molecular motors to demonstrate that a multivalent catalytic walker with flexible, uncoordinated legs can transform the free energy of surface-bound substrate sites into mechanical work and undergo…
In many biochemical processes, proteins bound to DNA at distant sites are brought into close proximity by loops in the underlying DNA. For example, the function of some gene-regulatory proteins depends on such DNA looping interactions. We…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…
We investigate irreversibility and dissipation in single molecules that cooperatively fold/unfold in a two state manner under the action of mechanical force. We apply path thermodynamics to derive analytical expressions for the average…
The translocation of structured RNA or DNA molecules through narrow pores necessitates the opening of all base pairs. Here, we study the interplay between the dynamics of translocation and base-pairing theoretically, using kinetic Monte…
Dimeric molecular motors walk on polar tracks by binding and hydrolyzing one ATP per step. Despite tremendous progress, the waiting state for ATP binding in the well-studied kinesin that walks on microtubule (MT), remains controversial. One…
We propose a new toy model of a heteropolymer chain capable of forming planar secondary structures typical for RNA molecules. In this model the sequential intervals between neighboring monomers along a chain are considered as quenched…
We introduce and train distributed neural architectures (DNA) in vision and language domains. DNAs are initialized with a proto-architecture that consists of (transformer, MLP, attention, etc.) modules and routers. Any token (or patch) can…
In this study, through phenomenological comparison of the velocity-force data of processive motor proteins, including conventional kinesin, cytoplasmic dynein and myosin V, we found that, the ratio between motor velocities of two different…
In this paper, we investigate a stochastic model describing the time evolution of a polymerization process. A polymer is a macro-molecule resulting from the aggregation of several elementary sub-units called monomers. Polymers can grow by…
DNA renaturation is the recombination of two complementary single strands to form a double helix. It is experimentally known that renaturation proceeds through the formation of a double stranded nucleus of several base pairs (the rate…
Cats use the connection governing parallel transport in the space of shapes to land safely on their feet. Here we argue that this connection also explains the impressive performance of molecular motors by enabling molecules to evade…
We present a study of the DNA translocation of the bacteriophage \phi 29 packaging molecular motor. From the experimental available information we present a model system based in an stochastic fashing potential, which reproduces the…
We explore and quantify the physical and biochemical mechanisms that may be relevant in the regulation of translation. After elongation and detachment from the 3' termination site of mRNA, parts of the ribosome machinery can diffuse back to…
We demonstrate a catalytic control method for speeding up the single-molecule DNA motor introduced by Li and Tan [Nano Lett. {\bf 2}, 315 (2002)]. A key rate-limiting barrier in the reaction part of the cycle is the tendency for the second…
We develop a method for solving mathematical models of messenger RNA (mRNA) translation based on the totally asymmetric simple exclusion process (TASEP). Our main goal is to demonstrate that the method is versatile and applicable to…
Inspired by dimeric motor proteins capable of undergoing transportation in living cells, significant efforts have been expended to the fabrication of track-walking nanomotors possessing two foot-like components that each can bind or detach…
First principle calculations of charge transfer in DNA molecules are computationally expensive given that charge carriers migrate in interaction with intra- and inter-molecular atomic motion. Screening sequences, e.g. to identify excellent…