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The fidelity of DNA replication by DNA polymerase (DNAP) has long been an important issue in biology. While numerous experiments have revealed details of the molecular structure and working mechanism of DNAP which consists of both a…
Molecular biology explains function of molecules by their geometrical and electronical structures that are mainly determined by utilization of quantum effects in chemistry. However, further quantum effects are not thought to play any…
Chromatin remodeling machineries are abundant and diverse in eukaryotic cells. They have been involved in a variety of situations such as histone exchange and DNA repair, but their importance in gene expression remains unclear. Although the…
Understanding the operation of biological molecular motors, nanoscale machines that transduce electrochemical energy into mechanical work, is enhanced by bottom-up strategies to synthesize novel motors.
Synthetic methods to control the structure of materials at sub-micron scales are typically based on the self-assembly of structural building blocks with precise size and morphology. On the other hand, many living systems can generate…
A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a…
Eukaryotic cells and intracellular pathogens such as bacteria or viruses utilize the actin polymerization machinery to propel themselves forward. Thereby, the onset of motion and choice of direction may be the result of a spontaneous…
This paper presents the implementation of a self-replicating finite-state machine (FSM) and a self-replicating Turing Machine (TM) using bio-inspired mechanisms. Building on previous work that introduced self-replicating structures capable…
The transport of deformable particles through porous media underlies a wealth of applications ranging from filtration to oil recovery to the transport and spreading of biological agents. Using direct numerical simulations, we analyze the…
Cell spreading is investigated at various scales in order to understand motility of living cells which is essential for a range of physiological activities in higher organisms as well as in microbes. At a microscopic scale, it has been seen…
Although non-canonical residues, caps, crosslinks, and nicks play an important role in the function of many DNA, RNA, proteins, and complexes, we do not fully understand how networks of non-canonical macromolecules generate behavior. One…
The molecular polarizability describes the tendency of a molecule to deform or polarize in response to an applied electric field. As such, this quantity governs key intra- and inter-molecular interactions such as induction and dispersion,…
Functionalization of nanoparticles or colloids is increasingly being used to develop customizable "atoms". Functionalization by attaching single strands of DNA allows for direct control of the binding between nanoparticles, since…
Polymer architecture plays critical roles in both bulk rheological properties and microscale macromolecular dynamics in entangled polymer solutions and composites. Ring polymers, in particular, have been the topic of much debate due to the…
DNA and Carbon nanotubes (CNTs) have unique physical, mechanical and electronic properties that make them revolutionary materials for advances in technology. In state-of-the-art applications, these physical properties can be exploited to…
Molecular biology is a nanotechnology that works--it has worked for billions of years and in an amazing variety of circumstances. At its core is a system for acquiring, processing and communicating information that is universal, from…
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…
The interactions between DNA, RNA, and proteins are fundamental to biological processes, as illustrated by the central dogma of molecular biology. Although modern biological pre-trained models have achieved great success in analyzing these…
Most widely used machine learned (ML) potentials for condensed phase applications rely on many-body permutationally invariant polynomial (PIP) or atom-centered neural networks (NN). However, these approaches often lack chemical…
The question of how stiff polymers are able to pack into small containers is particularly relevant to the study of DNA packaging in viruses. A reduced version of the problem based on coarse-grained representations of the main components of…