Related papers: ATP-Dependent Mismatch Recognition in DNA Replicat…
Considering a multi-pathway structure in a light-harvesting complex of photosynthesis, we investigate the role of energy-level mismatches between antenna molecules in transferring the absorbed energy to a reaction center. We find a…
Damaged or mismatched bases in DNA can be repaired by Base Excision Repair (BER) enzymes that replace the defective base. Although the detailed molecular structures of many BER enzymes are known, how they colocalize to lesions remains…
Base-pockets (non-complementary base-pairs) in a double-stranded DNA play a crucial role in biological processes. Because of thermal fluctuations, it can lower the stability of DNA, whereas, in case of DNA aptamer, small molecules e.g.…
We introduce an approach to detecting inconsistencies in large biological networks by using Answer Set Programming (ASP). To this end, we build upon a recently proposed notion of consistency between biochemical/genetic reactions and…
ATP synthase's intrinsic molecular electrostatic potential (MESP) adds constructively to, and hence reinforces, the chemiosmotic voltage. This ATP synthase voltage represents a new free energy term that appears to have been overlooked. This…
Hydrogen atom transfer (HAT) reactions are essential in many biological processes, such as radical migration in damaged proteins, but their mechanistic pathways remain incompletely understood. Simulating HAT is challenging due to the need…
We analyze mismatch in the inverse-squeezing Kennedy receiver for binary displaced squeezed vacuum state discrimination. Mismatch is shown to be equivalent to a residual squeezing after nulling, which modifies the output photon-number…
CRISPR-Cas is an adaptive immune mechanism that has been harnessed for a variety of genetic engineering applications: the Cas9 protein recognises a 2-5nt DNA motif, known as the PAM, and a programmable crRNA binds a target DNA sequence that…
We demonstrate a new algorithm for finding protein conformations that minimize a non-bonded energy function. The new algorithm, called the difference map, seeks to find an atomic configuration that is simultaneously in two constraint…
Fueled by the hydrolysis of ATP, the motor protein kinesin literally walks on two legs along the biopolymer microtubule. The number of accidental backsteps that kinesin takes appears to be much larger than what one would expect given the…
Unlike primates, training artificial neural networks on changing data distributions leads to a rapid decrease in performance on old tasks. This phenomenon is commonly referred to as catastrophic forgetting. In this paper, we investigate the…
For multi-level systems in hot atomic vapors the interplay between the Doppler shift due to atom velocity and the wavenubmer mismatch between driving laser fields strongly influences transmission and absorption properties of the atomic…
In this paper we investigate the \emph{approximate string matching problem} when the allowed edit operations are \emph{non-overlapping unbalanced translocations of adjacent factors}. Such kind of edit operations take place when two adjacent…
The aim of the present work is spectroscopic and thermodynamic study of DNA catalytic properties in the following processes: a) redox; b) formation of inter-strand cross-links; c) performing of photo-dynamic effects; d) nanoscale resonance…
Understanding the thermodynamics of the duplication process is a fundamental step towards a comprehensive physical theory of biological systems. However, the immense complexity of real cells obscures the fundamental tensions between energy…
Gene expression and regulation rely on an apparently finely tuned set of reactions between some proteins and DNA. Such DNA-binding proteins have to find specific sequences on very long DNA molecules and they mostly do so in absence of any…
Tandem repeats in proteins identification, classification and curation is a complex process that requires manual processing from experts, processing power and time. There are recent and relevant advances applying machine learning for…
At present, there have been suggested two types of physical mechanism that may facilitate preferential pairing between DNA molecules, with identical or similar base pair texts, without separation of base pairs. One solely relies on base…
The computational study of conformational transitions in nucleic acids still faces many challenges. For example, in the case of single stranded RNA tetranucleotides, agreement between simulations and experiments is not satisfactory due to…
Gel electrophoresis, a widely used technique to separate DNA according to their size and weight, generates images that can be analyzed automatically. Manual or semiautomatic image processing presents a bottleneck for further development and…