Related papers: Theoretical Perspectives on Biological Machines
Increasingly sophisticated experiments, coupled with large-scale computational models, have the potential to systematically test biological hypotheses to drive our understanding of multicellular systems. In this short review, we explore key…
We review the status of protein-based molecular electronics. First we discuss fundamental concepts of electron transfer and transport in and across proteins and proposed mechanisms for these processes. We then describe the immobilization of…
Molecular machines composed of coupled subsystems transduce free energy between different external reservoirs, in the process internally transducing energy and information. While subsystem efficiencies of these molecular machines have been…
Machine learning (ML) is transforming all areas of science. The complex and time-consuming calculations in molecular simulations are particularly suitable for a machine learning revolution and have already been profoundly impacted by the…
Molecular motors convert chemical energy into mechanical work while operating in an environment dominated by Brownian motion. The aim of this paper is to explore the flow of energy between the molecular motors and its surroundings, in…
Molecular chaperones are ATP-consuming biological machines, which facilitate the folding of proteins and RNA molecules that are kinetically trapped in misfolded states for long times. Unassisted folding occurs by the kinetic partitioning…
Biological functions stem from coordinated interactions among proteins, nucleic acids and small molecules. Mass spectrometry technologies for reliable, high throughput single-cell proteomics will add a new modality to genomics and enable…
Single-molecule biophysics has transformed our understanding of the fundamental molecular processes involved in living biological systems, but also of the fascinating physics of life. Far more exotic than a collection of exemplars of soft…
One of the important challenges facing high resolution molecular dynamics calculations is to reproduce biological functions that occur in the macroscopic world and involve macroscopic variables. Some of these functions can be well described…
The stochastic driving force exerted by a single molecular motor (e.g., a kinesin, or myosin) moving on a periodic molecular track (microtubule, actin filament, etc.) is discussed from a general viewpoint open to experimental test. An…
The present view of biological phenomena is based on a biochemical paradigm that development of living organisms is defined by information stored in a molecular form as some genetic code. However, new discoveries indicate that biological…
It is a fascinating subject to explore how well we can understand the processes of life on the basis of fundamental laws of physics. It is emphasised that viewing biological processes as manipulation of information extracts their essential…
Systems biology and whole-cell modelling are demanding increasingly comprehensive mathematical models of cellular biochemistry. These models require the development of simplified models of specific processes which capture essential…
Recently, microRNAs (miRNAs) have emerged as central posttranscriptional regulators of gene expression. miRNAs regulate many key biological processes, including cell growth, death, development and differentiation. This discovery is…
To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…
We examine the dependence of the physical quantities of the rotatory molecular motor, such as the rotation velocity and the proton translocation rate, on the chemical reaction rate using the model based only on diffusion process. A peculiar…
Motor-driven cargo transport is a complex phenomenon where multiple motor proteins attached on to a cargo engage in pulling activity, often leading to tug-of-war, displaying bidirectional motion. However, most mathematical and computational…
Molecular chaperones play a prominent role in signaling and transcriptional regulatory networks of the cell. Recent advances uncovered that chaperones act as genetic buffers stabilizing the phenotype of various cells and organisms and may…
Traffic-like collective movements are observed at almost all levels of biological systems. Molecular motor proteins like, for example, kinesin and dynein, which are the vehicles of almost all intra-cellular transport in eukayotic cells,…
In multicellular organisms, relations among parts and between parts and the whole are contextual and interdependent. These organisms and their cells are ontogenetically linked: an organism starts as a cell that divides producing…