作者: Affiliation 時(shí)間: 2025-3-21 23:36 作者: innovation 時(shí)間: 2025-3-22 02:35
Lecture Notes in Computational Science and Engineeringhttp://image.papertrans.cn/c/image/232847.jpg作者: 消耗 時(shí)間: 2025-3-22 07:58 作者: dermatomyositis 時(shí)間: 2025-3-22 11:21 作者: 符合你規(guī)定 時(shí)間: 2025-3-22 13:19 作者: 符合你規(guī)定 時(shí)間: 2025-3-22 18:54 作者: gastritis 時(shí)間: 2025-3-22 21:40
Fast Random Cactus Graph Generationroscopic processes. Unfortunately, such MD simulations require an enormous amount of computer time and, therefore, are limited to time scales of nanoseconds. We describe first a fast multiple time step structure adapted multipole method (FAMUSAMM) to speed up the evaluation of the computationally mo作者: Mangle 時(shí)間: 2025-3-23 02:47 作者: mastoid-bone 時(shí)間: 2025-3-23 07:26
Panel Discussion 1: Questions and Answersr system is considered as an open system. The model describes the transitions between three main conformations of wet nucleic acid samples: A-, B- and unordered forms. The analysis of kinetic equations shows the non-trivial bifurcation behaviour of the system which leads to the multistability. This 作者: 吹牛大王 時(shí)間: 2025-3-23 10:35
Scientific Investigations by Supercomputingal approaches used to characterize the interactions between proteins and small molecules: equilibrium measurement of binding constant and standard free energy of binding and the dynamic approach of ligand extraction via atomic force microscopy. Next, the paper reviews ideas about the origin of diffe作者: 詩(shī)集 時(shí)間: 2025-3-23 14:35
Supercomputing of Incompressible Fluid Flow initial state, make an assumption in regard to the functional form of the free energy or treat the mutation as a single step perturbation. Of these the perturbation approach holds the greatest promise. The perturbation approach is fast, easy to implement and does not depend on empirically derived p作者: 魅力 時(shí)間: 2025-3-23 21:18 作者: Alveoli 時(shí)間: 2025-3-24 01:07
J. M. Ramírez-Velásquez,Jennifer A. Sanchez based on an assumption that the difference in protonation behavior of a given group in an isolated state in solution, for which the ionization constant is assumed to be known, and the protonation behavior in the protein environment is purely electrostatic in origin. Calculations of the relevant ele作者: 異常 時(shí)間: 2025-3-24 05:53
Sergio Nesmachnow,Santiago Iturriagaeneralization of the law of mass action is used to derive equilibrium constants. Reaction rate constants for barrier crossing are derived using the transition state theory approximation. Monte Carlo and Molecular Dynamics algorithms which can be used to sample Tsallis statistical distributions are d作者: Fibrinogen 時(shí)間: 2025-3-24 06:38
J. M. Ramírez-Velásquez,Joshua M. Salazar the distances between the .. atoms of a protein. The potential is a sum of smooth surface potential terms that model solvent interactions and of pair potentials that are functions of a distance, with a smooth cutoff at 12 ?ngstr?m. Techniques include the use of a fully automatic and reliable estima作者: 金桌活畫(huà)面 時(shí)間: 2025-3-24 13:31
Ivan Zhuravlev,Andrey Makarenkoious approaches. These approaches include implicit discretization, separation into harmonic and anharmonic motion, and force splitting; some of these techniques are combined with stochastic dynamics. A Langevin/force-splitting approach for biomolecular simulations termed LN (for its origin in a Lang作者: scrape 時(shí)間: 2025-3-24 17:52 作者: 使腐爛 時(shí)間: 2025-3-24 21:55 作者: FUSE 時(shí)間: 2025-3-25 02:58 作者: Ptosis 時(shí)間: 2025-3-25 07:03 作者: 陶瓷 時(shí)間: 2025-3-25 08:44
1439-7358 in. The event brought together computational scientists in fields like biochemistry, biophysics, physical chemistry, or statistical physics and numerical analysts as well as computer scientists working on the advancement of algorithms, for a total of over 120 participants from 19 countries. In the c作者: 華而不實(shí) 時(shí)間: 2025-3-25 12:46 作者: innate 時(shí)間: 2025-3-25 19:50 作者: kyphoplasty 時(shí)間: 2025-3-25 23:17
Mathematical Model of the Nucleic Acids Conformational Transitions with Hysteresis over Hydration—Defact allows one to explain the hysteresis phenomena observed experimentally in the nucleic acid-water system. The problem of self-organization in the nucleic acid-water system is of great importance for revealing physical mechanisms of the functioning of nucleic acids and for many specific practical fields.作者: Haphazard 時(shí)間: 2025-3-26 03:39 作者: 外來(lái) 時(shí)間: 2025-3-26 05:20 作者: rheumatism 時(shí)間: 2025-3-26 11:07
On Some Difficulties in Integrating Highly Oscillatory Hamiltonian Systemsble, semi-implicit methods. Here semi-implicit means that only the highly oscillatory part is integrated by an implicit method such as the midpoint method or an energy-conserving variant of it. The hope is that such methods will allow one to use a step-size . which is much larger than the period . of the fast oscillations.作者: engrave 時(shí)間: 2025-3-26 12:41 作者: 祝賀 時(shí)間: 2025-3-26 20:48
S. Ivvan Valdez,Felipe Trujillo-Romeroependent protein kinase (cAPK) with a continuum (Poisson) model for the electrostatics. In this paper, we will put the previous results into context and discuss possible extensions into the dynamic regime.作者: 粗糙濫制 時(shí)間: 2025-3-26 23:23 作者: liposuction 時(shí)間: 2025-3-27 01:31
Conformational Transitions of Proteins from Atomistic Simulationsependent protein kinase (cAPK) with a continuum (Poisson) model for the electrostatics. In this paper, we will put the previous results into context and discuss possible extensions into the dynamic regime.作者: 宏偉 時(shí)間: 2025-3-27 07:36 作者: Agronomy 時(shí)間: 2025-3-27 11:31
Nikolai Zamarashkin,Dmitry Zheltkovrticle densities rather than positions. It is concluded that MD is a mature technique for classical simulations of all-atom systems in the nanosecond time range, but is still in its infancy in reaching reliably into longer time scales.作者: Bumptious 時(shí)間: 2025-3-27 14:53 作者: confide 時(shí)間: 2025-3-27 20:30
Molecular Dynamics Simulations: The Limits and Beyondrticle densities rather than positions. It is concluded that MD is a mature technique for classical simulations of all-atom systems in the nanosecond time range, but is still in its infancy in reaching reliably into longer time scales.作者: 提煉 時(shí)間: 2025-3-27 22:59
New Techniques for the Construction of Residue Potentials for Protein Foldingfind appropriate weights with which the various terms enter the total potential. For nine small test proteins, the new potential has local minima within 1.3-4.7? of the PDB geometry, with one exception that has an error of 8.5?.作者: BUST 時(shí)間: 2025-3-28 02:26
Moises Torres,Jaime Klapp,Andrei Tchernykhays to explanation of elastic properties of proteins. First attempts to deduce potentials of mean force by discounting irreversible work performed on the system are summarized. The non-equilibrium statistical mechanics underlying analysis of SMD data is outlined.作者: Fermentation 時(shí)間: 2025-3-28 06:29
Fast Random Cactus Graph Generationst demanding Coulomb interactions in solvated protein models, secondly an application of this method aiming at a microscopic understanding of single molecule atomic force microscopy experiments, and, thirdly, a new method to predict slow conformational motions at microsecond time scales.作者: Ostrich 時(shí)間: 2025-3-28 10:38
Panel Discussion 1: Questions and Answersfact allows one to explain the hysteresis phenomena observed experimentally in the nucleic acid-water system. The problem of self-organization in the nucleic acid-water system is of great importance for revealing physical mechanisms of the functioning of nucleic acids and for many specific practical fields.作者: Rebate 時(shí)間: 2025-3-28 17:50 作者: 輕打 時(shí)間: 2025-3-28 20:18 作者: Cpr951 時(shí)間: 2025-3-29 00:45
https://doi.org/10.1007/978-3-030-64616-5ble, semi-implicit methods. Here semi-implicit means that only the highly oscillatory part is integrated by an implicit method such as the midpoint method or an energy-conserving variant of it. The hope is that such methods will allow one to use a step-size . which is much larger than the period . of the fast oscillations.作者: Ibd810 時(shí)間: 2025-3-29 04:35
Computational Molecular Dynamics: Challenges, Methods, IdeasProceeding of the 2n作者: 分解 時(shí)間: 2025-3-29 09:34
Computation of Essential Molecular Dynamics by Subdivision Techniquesctory simulation on the other hand: in our setup long term trajectories are replaced by short term sub-trajectories, Monte-Carlo techniques are connected via the underlying Frobenius-Perron structure. Numerical experiments with the suggested algorithm are included to illustrate certain distinguishin作者: 易于出錯(cuò) 時(shí)間: 2025-3-29 14:18 作者: 女上癮 時(shí)間: 2025-3-29 19:31
Exploration of Peptide Free Energy Surfacesminima are further refined by the novel procedure of free energy optimization by steepest descent down the gradient, leading to structures in excellent agreement with experimental data. The stability of the minima with respect to deformations is studied by analysis of second derivatives of the free 作者: tic-douloureux 時(shí)間: 2025-3-29 23:24
Prediction of pKas of Titratable Residues in Proteins Using a Poisson-Boltzmann Model of the Solute-ow-energy ionization states out of all possible states, to obtain a correct estimation of thermodynamic properties of the system..As examples of applications, we present the overall accuracy of predicted ionization constants for about 50 groups in 4 proteins, changes in the average charge of bovine 作者: Cpap155 時(shí)間: 2025-3-30 03:15 作者: Alveoli 時(shí)間: 2025-3-30 07:46 作者: keloid 時(shí)間: 2025-3-30 10:22
Scientific Investigations by Supercomputings inside proteins, (2) calculation of binding free energy from “first principles” by a new application of molecular transformation, and (3) extraction of a small ligand (xenon) from a hydrophobic cavity in mutant T4-lysozyme L99A.作者: 離開(kāi)就切除 時(shí)間: 2025-3-30 13:15 作者: GET 時(shí)間: 2025-3-30 20:02 作者: 根除 時(shí)間: 2025-3-30 20:48
Molecular Dynamics Simulations: The Limits and Beyond is given of methods, algorithms and force fields. After considering the limitations of the standard present-day techniques, developments that reach beyond the present limitations are considered. These concern three major directions: (a) inclusion of quantum dynamics, (b) reduction of complexity by 作者: minaret 時(shí)間: 2025-3-31 01:04
Steered Molecular Dynamicscs simulations. Time-dependent external forces are applied to a system, and the responses of the system are analyzed. SMD has already provided important qualitative insights into biologically relevant problems, as demonstrated here for applications ranging from identification of ligand binding pathw作者: FLOUR 時(shí)間: 2025-3-31 05:57
Conformational Transitions of Proteins from Atomistic Simulationsll loop movements that allow access to the protein’s active site, or large movements such as those of motor proteins that are implicated with muscular extension. Yet, in spite of the increasing number of three-dimensional crystal structures of proteins in different conformations, not much is known a
