Biophysics is an interdisciplinary science that applies approaches and methods traditionally used in physics to study biological phenomena. Biophysics covers all scales of biological organization, from molecular to organismic and populations. Biophysical research shares significant overlap with biochemistry, molecular biology, physical chemistry, physiology, nanotechnology, bioengineering, computational biology, biomechanics, developmental biology and systems biology.
Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields. The method is applied mostly in chemical physics, materials science, and biophysics.
Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system. The common feature of molecular modelling methods is the atomistic level description of the molecular systems. This may include treating atoms as the smallest individual unit, or explicitly modelling protons and neutrons with its quarks, anti-quarks and gluons and electrons with its photons.
B. Montgomery "Monte" Pettitt is the Director of the Sealy Center for Structural Biology and Molecular Biophysics at University of Texas Medical Branch in Galveston, Texas, holder of the Robert A. Welch Distinguished Chair in Chemistry, and tenured Professor in the Department of Biochemistry and Molecular Biology, as well as the department of Pharmacology and Toxicology. He is also affiliated with and former director of The W. M. Keck Center at Rice University, and a faculty member of the Structural and Computational Biology and Molecular Biophysics program at Baylor College of Medicine. At the University of Houston, he was the Hugh Roy and Lille Cranz Cullen Distinguished Professor of Chemistry and Robert A. Welch Chair in Chemistry, as well as the director of its Institute for Molecular Design.
The Max Planck Institute for Biophysical Chemistry, also known as the Karl-Friedrich Bonhoeffer Institute, was a research institute of the Max Planck Society, located in Göttingen, Germany. On January 1, 2022, the institute merged with the Max Planck Institute for Experimental Medicine in Göttingen to form the Max Planck Institute for Multidisciplinary Sciences.
In the context of chemistry, molecular physics, physical chemistry, and molecular modelling, a force field is a computational model that is used to describe the forces between atoms within molecules or between molecules as well as in crystals. Force fields are a variety of interatomic potentials. More precisely, the force field refers to the functional form and parameter sets used to calculate the potential energy of a system on the atomistic level. Force fields are usually used in molecular dynamics or Monte Carlo simulations. The parameters for a chosen energy function may be derived from classical laboratory experiment data, calculations in quantum mechanics, or both. Force fields utilize the same concept as force fields in classical physics, with the main difference being that the force field parameters in chemistry describe the energy landscape on the atomistic level. From a force field, the acting forces on every particle are derived as a gradient of the potential energy with respect to the particle coordinates.
Benoît Roux is an Amgen Professor of Biochemistry and Molecular Biophysics at the University of Chicago. He has previously taught at University of Montreal and Weill Medical College of Cornell University. Benoît Roux was a recipient of the 1998 Rutherford Memorial Medal in Chemistry, awarded by the Royal Society of Canada.
DNA supercoiling refers to the amount of twist in a particular DNA strand, which determines the amount of strain on it. A given strand may be "positively supercoiled" or "negatively supercoiled". The amount of a strand's supercoiling affects a number of biological processes, such as compacting DNA and regulating access to the genetic code. Certain enzymes, such as topoisomerases, change the amount of DNA supercoiling to facilitate functions such as DNA replication and transcription. The amount of supercoiling in a given strand is described by a mathematical formula that compares it to a reference state known as "relaxed B-form" DNA.
Molecular biophysics is a rapidly evolving interdisciplinary area of research that combines concepts in physics, chemistry, engineering, mathematics and biology. It seeks to understand biomolecular systems and explain biological function in terms of molecular structure, structural organization, and dynamic behaviour at various levels of complexity. This discipline covers topics such as the measurement of molecular forces, molecular associations, allosteric interactions, Brownian motion, and cable theory. Additional areas of study can be found on Outline of Biophysics. The discipline has required development of specialized equipment and procedures capable of imaging and manipulating minute living structures, as well as novel experimental approaches.
Stephen Levene is an American biophysicist and professor of bioengineering, molecular biology, and physics at the University of Texas at Dallas.
CP2K is a freely available (GPL) quantum chemistry and solid state physics program package, written in Fortran 2008, to perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. It provides a general framework for different methods: density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW) via LDA, GGA, MP2, or RPA levels of theory, classical pair and many-body potentials, semi-empirical and tight-binding Hamiltonians, as well as Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid schemes relying on the Gaussian Expansion of the Electrostatic Potential (GEEP). The Gaussian and Augmented Plane Waves method (GAPW) as an extension of the GPW method allows for all-electron calculations. CP2K can do simulations of molecular dynamics, metadynamics, Monte Carlo, Ehrenfest dynamics, vibrational analysis, core level spectroscopy, energy minimization, and transition state optimization using NEB or dimer method.
In computer software, Orac is a classical molecular dynamics program, to simulate complex molecular systems at the atomistic level. In 1989-1990, the code was written originally by Massimo Marchi during his stay at International Business Machines (IBM), Kingston (USA). In 1995, the code was developed further at the Centre européen de calcul atomique et moléculaire (CECAM). It is written in the programming language Fortran. In 1997, it was released under a GNU General Public License (GPL). The latest release of Orac may be run in parallel using the standard Message Passing Interface (MPI) libraries, allowing replica exchange simulations, multiple walkers metadynamics simulations and multiple steered molecular dynamics nonequilibrium trajectories.
Edward Nikolayevich Trifonov is a Russian-born Israeli molecular biophysicist and a founder of Israeli bioinformatics. In his research, he specializes in the recognition of weak signal patterns in biological sequences and is known for his unorthodox scientific methods.
Adaptive sampling is a technique used in computational molecular biology to efficiently simulate protein folding when coupled with molecular dynamics simulations.
Klaus Schulten was a German-American computational biophysicist and the Swanlund Professor of Physics at the University of Illinois at Urbana-Champaign. Schulten used supercomputing techniques to apply theoretical physics to the fields of biomedicine and bioengineering and dynamically model living systems. His mathematical, theoretical, and technological innovations led to key discoveries about the motion of biological cells, sensory processes in vision, animal navigation, light energy harvesting in photosynthesis, and learning in neural networks.
Marta Filizola is a computational biophysicist who studies membrane proteins. Filizola's research concerns drug discovery the application of methods of computational chemistry and theoretical chemistry to biochemical and biomedical problems.
Florian Müller-Plathe is a German theoretical chemist and professor for theoretical physical chemistry at Technische Universität Darmstadt.
Karissa Y. Sanbonmatsu is an American structural biologist at Los Alamos National Laboratory. She works on the mechanism of non-coding RNA complexes including the ribosome, riboswitches, long non-coding RNAs, as well as chromatin. She was the first to perform an atomistic simulation of the ribosome, determine the secondary structure of an intact lncRNA and to publish a one billion atom simulation of a biomolecular complex.
Syma Khalid is a British Scientist who is a Professor of Computational Microbiology in at the University of Oxford. She was awarded the Suffrage Science award for engineering and physical sciences in 2021.
The Ascona B-DNA Consortium (ABC) is a collaborative international research initiative founded in 2001 to investigate the sequence-dependent mechanical properties of DNA using molecular dynamics (MD) simulations. The consortium has contributed significantly to the understanding of DNA structure and dynamics over the past two decades, from the atomic level to larger chromatin structures. The ABC's work includes the development of simulation standards, force fields, and data libraries for DNA, enabling the systematic study of sequence effects across different nucleotide configurations.
