Related papers: ATP-Dependent Mismatch Recognition in DNA Replicat…
Key enzymatic processes in biology use the nonequilibrium error correction mechanism called kinetic proofreading to enhance their specificity. Kinetic proofreading typically requires several dedicated structural features in the enzyme, such…
We discuss the role of water bridging the DNA-enzyme interaction by resorting to recent results showing that London dispersion forces between delocalized electrons of base pairs of DNA are responsible for the formation of dipole modes that…
Atom probe tomography (APT) is a 3D analysis technique that offers unique chemical accuracy and sensitivity with sub-nanometer spatial resolution. Recently, there is an increasing interest in the application of APT to complex oxides…
We evaluate the quantum resource requirements for ATP/metaphosphate hydrolysis, one of the most important reactions in all of biology with implications for metabolism, cellular signaling, and cancer therapeutics. In particular, we consider…
Searching through chemical space is an exceptionally challenging problem because the number of possible molecules grows combinatorially with the number of atoms. Large, autoregressive models trained on databases of chemical compounds have…
The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated…
Specific binding of proteins to DNA is one of the most common ways in which gene expression is controlled. Although general rules for the DNA-protein recognition can be derived, the ambiguous and complex nature of this mechanism precludes a…
Determining the interaction strength between proteins and small molecules is key to analyzing their biological function. Quantum-mechanical calculations such as \emph{Density Functional Theory} (DFT) give accurate and theoretically…
Expressing the energy content of food as the heat energy released by its combustion is potentially misleading. Food is used to produce adenosine triphosphate (ATP). The free energy of conversion of ATP into adenosine diphosphate is used…
This paper reports a modified axiomatic foundation of the analytic hierarchy process (AHP), where the reciprocal property of paired comparisons is broken. The novel concept of reciprocal symmetry breaking is proposed to characterize the…
DNA replication fidelity is a critical issue in molecular biology. Biochemical experiments have provided key insights on the mechanism of fidelity control by DNAP in the past decades, whereas systematic theoretical studies on this issue…
Enhanced sampling techniques are essential for exploring biomolecular conformational dynamics that occur on timescales inaccessible to conventional molecular dynamics (MD) simulations. This study introduces a framework that combines…
We propose a new analytical potential function to model proton transfer in the adenine-thymine base pair and develop a non-adiabatic quantum mechanical framework to calculate genetic mutation probabilities. This potential has been used to…
The interaction energies between the different types of bases of a single strand of DNA molecule have been calculated. Using these original values of energies the harmonic behavior of a number of base patterns of DNA has been studied. In…
Biological processes such as DNA replication, RNA transcription, and protein translation show remarkable speed and accuracy in selecting the right substrate from pools of chemically identical molecules. This result is obtained by…
Hsp70 molecular chaperones are abundant ATP-dependent nanomachines that actively reshape non-native, misfolded proteins and assist a wide variety of essential cellular processes. Here we combine complementary computational/theoretical…
Fast, reliable and inexpensive DNA sequencing is an important pursuit in healthcare, especially in personalized medicine with possible deep societal impacts. Despite significant progress of various nanopore-based sequencing configurations,…
To sustain metabolism, intracellular ATP concentration must be regulated within an appropriate range. This coordination is achieved through the function of the AMP-activated protein kinase (AMPK), a cellular "fuel gauge" that is expressed…
Physics-based and first-principles models pervade the engineering and physical sciences, allowing for the ability to model the dynamics of complex systems with a prescribed accuracy. The approximations used in deriving governing equations…
Complementary strands in DNA double helix show temporary fluctuational openings which are essential to biological functions such as transcription and replication of the genetic information. Such large amplitude fluctuations, known as the…