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Dan T. Major
Dr. Dan Thomas Major ( he, דן מאיור; born 22 March 1973) is a Professor of Chemistry at Bar Ilan University specializing in Computational Chemistry. Biography Dan Major obtained his Ph.D. from the Chemistry Department at Bar-Ilan University (BIU) in 2003, followed by three years as a postdoctoral fellow at the University of Minnesota working with Prof. Jiali Gao. In 2007 he moved to the Chemistry Department at Bar-Ilan University, where he is now a full professor. Scientific interests and publications Major's research focuses on computational approaches to chemistry, biochemistry, and nanotechnology. These include the development of simulation methods, a study of enzyme reactions and protein dynamics, understanding natural product synthesis, development of protein-ligand docking programs, in silico design of Li-ion batteries, and fuel cell modeling. He develops classical and quantum simulation methods, and in particular tools for studying enzyme catalysis. This ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Norway
Norway, officially the Kingdom of Norway, is a Nordic country in Northern Europe, the mainland territory of which comprises the western and northernmost portion of the Scandinavian Peninsula. The remote Arctic island of Jan Mayen and the archipelago of Svalbard also form part of Norway. Bouvet Island, located in the Subantarctic, is a dependency of Norway; it also lays claims to the Antarctic territories of Peter I Island and Queen Maud Land. The capital and largest city in Norway is Oslo. Norway has a total area of and had a population of 5,425,270 in January 2022. The country shares a long eastern border with Sweden at a length of . It is bordered by Finland and Russia to the northeast and the Skagerrak strait to the south, on the other side of which are Denmark and the United Kingdom. Norway has an extensive coastline, facing the North Atlantic Ocean and the Barents Sea. The maritime influence dominates Norway's climate, with mild lowland temperatures on the se ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Dynamics
Proteins are generally thought to adopt unique structures determined by their amino acid sequences. However, proteins are not strictly static objects, but rather populate ensembles of (sometimes similar) conformations. Transitions between these states occur on a variety of length scales (tenths of Å to nm) and time scales (ns to s), and have been linked to functionally relevant phenomena such as allosteric signaling and enzyme catalysis. The study of protein dynamics is most directly concerned with the transitions between these states, but can also involve the nature and equilibrium populations of the states themselves. These two perspectives—kinetics and thermodynamics, respectively—can be conceptually synthesized in an "energy landscape" paradigm: highly populated states and the kinetics of transitions between them can be described by the depths of energy wells and the heights of energy barriers, respectively. Local flexibility: atoms and residues Portions of protein s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
QM/MM
The hybrid QM/MM (quantum mechanics/molecular mechanics) approach is a molecular simulation method that combines the strengths of ''ab initio'' QM calculations (accuracy) and MM (speed) approaches, thus allowing for the study of chemical processes in solution and in proteins. The QM/MM approach was introduced in the 1976 paper of Warshel and Levitt. They, along with Martin Karplus, won the 2013 Nobel Prize in Chemistry for "the development of multiscale models for complex chemical systems". Efficiency An important advantage of QM/MM methods is their efficiency. The cost of doing classical molecular mechanics (MM) simulations in the most straightforward case scales as ''O''(''N''2), where ''N'' is the number of atoms in the system. This is mainly due to electrostatic interactions term (every particle interacts with everything else). However, use of cutoff radius, periodic pair-list updates and more recently the variations of the particle mesh Ewald (PME) method has reduced this ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Docking (molecular)
In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when a ligand and a target are bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules using, for example, scoring functions. The associations between biologically relevant molecules such as proteins, peptides, nucleic acids, carbohydrates, and lipids play a central role in signal transduction. Furthermore, the relative orientation of the two interacting partners may affect the type of signal produced (e.g., agonism vs antagonism). Therefore, docking is useful for predicting both the strength and type of signal produced. Molecular docking is one of the most frequently used methods in structure-based drug design, due to its ability to predict the binding-conformation of small molecule ligands to the appropriate target bind ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Free Energy Perturbation
Free energy perturbation (FEP) is a method based on statistical mechanics that is used in computational chemistry for computing free energy differences from molecular dynamics or Metropolis Monte Carlo simulations. The FEP method was introduced by Robert W. Zwanzig in 1954. According to the free-energy perturbation method, the free energy difference for going from state A to state B is obtained from the following equation, known as the ''Zwanzig equation'': :\Delta F(\mathbf \rightarrow \mathbf) = F_\mathbf - F_\mathbf = -k_\mathrm T \ln \left \langle \exp \left ( - \frac \right ) \right \rangle _\mathbf where ''T'' is the temperature, ''k''B is Boltzmann's constant, and the angular brackets denote an average over a simulation run for state A. In practice, one runs a normal simulation for state A, but each time a new configuration is accepted, the energy for state B is also computed. The difference between states A and B may be in the atom types involved, in which case the Δ''F ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Quantum Tunnelling
Quantum tunnelling, also known as tunneling ( US) is a quantum mechanical phenomenon whereby a wavefunction can propagate through a potential barrier. The transmission through the barrier can be finite and depends exponentially on the barrier height and barrier width. The wavefunction may disappear on one side and reappear on the other side. The wavefunction and its first derivative are continuous. In steady-state, the probability flux in the forward direction is spatially uniform. No particle or wave is lost. Tunneling occurs with barriers of thickness around 1–3 nm and smaller. Some authors also identify the mere penetration of the wavefunction into the barrier, without transmission on the other side as a tunneling effect. Quantum tunneling is not predicted by the laws of classical mechanics where surmounting a potential barrier requires sufficient kinetic energy. Quantum tunneling plays an essential role in physical phenomena such as nuclear fusion and alpha radioact ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Zero-point Energy
Zero-point energy (ZPE) is the lowest possible energy that a quantum mechanical system may have. Unlike in classical mechanics, quantum systems constantly Quantum fluctuation, fluctuate in their lowest energy state as described by the Heisenberg uncertainty principle. Therefore, even at absolute zero, atoms and molecules retain some vibrational motion. Apart from atoms and molecules, the empty space of Vacuum state, the vacuum also has these properties. According to quantum field theory, the universe can be thought of not as isolated particles but continuous fluctuating Field (physics), fields: matter fields, whose Quantum, quanta are fermions (i.e., leptons and quarks), and Force field (physics), force fields, whose quanta are bosons (e.g., photons and gluons). All these fields have zero-point energy. These fluctuating zero-point fields lead to a kind of reintroduction of an Luminiferous aether, aether in physics since some systems can detect the existence of this energy. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Path Integral Formulation
The path integral formulation is a description in quantum mechanics that generalizes the action principle of classical mechanics. It replaces the classical notion of a single, unique classical trajectory for a system with a sum, or functional integral, over an infinity of quantum-mechanically possible trajectories to compute a quantum amplitude. This formulation has proven crucial to the subsequent development of theoretical physics, because manifest Lorentz covariance (time and space components of quantities enter equations in the same way) is easier to achieve than in the operator formalism of canonical quantization. Unlike previous methods, the path integral allows one to easily change coordinates between very different canonical descriptions of the same quantum system. Another advantage is that it is in practice easier to guess the correct form of the Lagrangian of a theory, which naturally enters the path integrals (for interactions of a certain type, these are ''coordinat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Enzyme Catalysis
Enzyme catalysis is the increase in the rate of a process by a biological molecule, an "enzyme". Most enzymes are proteins, and most such processes are chemical reactions. Within the enzyme, generally catalysis occurs at a localized site, called the active site. Most enzymes are made predominantly of proteins, either a single protein chain or many such chains in a multi-subunit complex. Enzymes often also incorporate non-protein components, such as metal ions or specialized organic molecules known as cofactor (e.g. adenosine triphosphate). Many cofactors are vitamins, and their role as vitamins is directly linked to their use in the catalysis of biological process within metabolism. Catalysis of biochemical reactions in the cell is vital since many but not all metabolically essential reactions have very low rates when uncatalysed. One driver of protein evolution is the optimization of such catalytic activities, although only the most crucial enzymes operate near catalytic e ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Modelling
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 (a molecular mechanics approach), or explicitly modelling protons and neutrons with its quarks, anti-quarks and gluons and electrons with its photons (a quantum chemistry approach). Molecular mechanics Molecular mechanics is one aspect of molecular modelling, as it involves the use of classical ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Fuel Cell
A fuel cell is an electrochemical cell that converts the chemical energy of a fuel (often hydrogen) and an oxidizing agent (often oxygen) into electricity through a pair of redox reactions. Fuel cells are different from most batteries in requiring a continuous source of fuel and oxygen (usually from air) to sustain the chemical reaction, whereas in a battery the chemical energy usually comes from substances that are already present in the battery. Fuel cells can produce electricity continuously for as long as fuel and oxygen are supplied. The first fuel cells were invented by Sir William Grove in 1838. The first commercial use of fuel cells came more than a century later following the invention of the hydrogen–oxygen fuel cell by Francis Thomas Bacon in 1932. The alkaline fuel cell, also known as the Bacon fuel cell after its inventor, has been used in NASA space programs since the mid-1960s to generate power for satellites and space capsules. Since then, fuel cells have b ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lithium-ion Battery
A lithium-ion or Li-ion battery is a type of rechargeable battery which uses the reversible reduction of lithium ions to store energy. It is the predominant battery type used in portable consumer electronics and electric vehicles. It also sees significant use for grid-scale energy storage and military and aerospace applications. Compared to other rechargeable battery technologies, Li-ion batteries have high energy densities, low self-discharge, and no memory effect (although a small memory effect reported in LFP cells has been traced to poorly made cells). Chemistry, performance, cost and safety characteristics vary across types of lithium-ion batteries. Most commercial Li-ion cells use intercalation compounds as the active materials. The anode or negative electrode is usually graphite, although silicon-carbon is also being increasingly used. Cells can be manufactured to prioritize either energy or power density. Handheld electronics mostly use lithium polymer batteries ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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