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Modeling Chemical Reactions in Enzymes and Solution with Proper Sampling:Using the Constrained DFT Approach in Generating Diabatic Surfaces

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Modeling Chemical Reactions in Enzymes and Solution with Pro...

Ursodeoxycholic acid and superoxide anion

中国化学会第九届全国量子化学学术会议

作者： Edina Rosta arieh warshel Department of Chemistry University of Southern California CA 90007USA Department of Chemistry University of Southern California CA 90007USA

＜正＞Modeling reactions in enzymes and solution have remained a major challenge for theoretical chemistry. One of the main problems has been associated with the difficulties of obtaining an appropriate sampling, which is essential for proper free energy calculations. The Empirical valence bond （EVB） method has been shown to provide significant advantages over other methods in

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World Journal of Gastroenterology 2005年第31期11卷 4875-4878页

作者： Predrag Ljubuncic Omar Abu-Salach arieh Bomzon Department of Pharmacology

AIM: To investigate the ability of ursodeoxycholic acid (UDCA) to scavenge superoxide anion (O2-).METHODS: We assessed the ability of UDCA to scavenge (O2-) generated by xanthine-xanthine oxidase (X-XO) in a cell-free system and its effect on the rate of O2--induced ascorbic acid (AA) oxidation in hepatic post-mitochondrial ***: UDCA at a concentration as high as 1 mmol/Ldid not impair the ability of the X-XO system to generate O2-, but could scavenge O2- at concentrations of 0.5 and 1 mmol/L, and decrease the rate of AA oxidation at a concentration of 100 μmol/***: UDCA can scavenge O2-, an action that may be beneficial to patients with primary biliary cirrhosis.

关键词： Ursodeoxycholic acid Superoxide anion Antioxidant

HIGHLY OSCILLATORY DIFFUSION-TYPE EQUATIONS

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Journal of Computational Mathematics 2013年第6期31卷 549-572页

作者： Sevda Uskiiplii Altlnbasak Marissa Condon Alfredo Deano arieh Iserles Department of Applied Mathematics and Theoretical Physics Centre for Mathematical Sciences University of Cambridge Cambridge UK School of Electronic Engineering Dublin City University Dublin Ireland Department of Mathematics University Carlos III de Madrid Madrid Spain Department of Applied Mathematics and Theoretical Physics Centre for Mathematical Sciences University of Cambridge Cambridge UK

We explore new asymptotic-numeric solvers for partial differential equations with highly oscillatory forcing terms. Such methods represent the solution as an asymptotic series, whose terms can be evaluated by solving non-oscillatory problems and they guarantee high accuracy at a low computational cost. We consider two forms of oscillatory forcing terms, namely when the oscillation is in time or in space： each lends itself to different treatment. Numerical examples highlight the salient features of the new approach.

关键词： Diffusion-type PDEs High oscillation Asymptotic expansions Modulated Fourier expansions.

Asymptotic solvers for ordinary differential equations with multiple frequencies

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Science China Mathematics 2015年第11期58卷 2279-2300页

作者： CONDON Marissa DEAO Alfredo GAO Jing ISERLES arieh School of Electronic Engineering Dublin City University Departmento de Matematicas Universidad Carlos III de Madrid School of Mathematics and Statistics Xi'an Jiaotong University DAMTP Centre for Mathematical SciencesUniversity of Cambridge

We construct asymptotic expansions for ordinary differential equations with highly oscillatory forcing terms,focusing on the case of multiple,non-commensurate *** derive an asymptotic expansion in inverse powers of the oscillatory parameter and use its truncation as an exceedingly effective means to discretize the differential equation in *** examples illustrate the effectiveness of the method.

关键词： highly oscillatory problems ordinary differential equation modulated Fourier expansions multiple frequencies numerical analysis

New experimental methodology to evaluate lubrication properties of synovial fluid containing worn tissue particles in osteoarthritis patients

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Friction 2023年第11期11卷 2132-2141页

作者： Israel DVIR Kareem ABD-RBO David SEGAL Leonid(arieh)KANDEL Haytam KASEM Department of Mechanical Engineering Azrieli College of EngineeringJerusalem 9103501Israel Department of Orthopedic Surgery Hadassah Mount Scopus HospitalJerusalem 9103501Israel

Studying the lubrication properties of osteoarthritis(OA)synovial fluid(SF)enables an understanding of the boundary lubrication joint,mobility,and ***,tribology has never been combined with the clinical reality of the presence of worn particles within the synovial fluid and how they affect the osteoarthritic *** of the problem relates to the tribology methods studying friction by applying inadequate pin-on-disc *** this study,synovial fluid with and without worn particles was studied using a customized *** method enables opening the contact at the end of each cycle and simulates better contact conditions of a natural knee joint and can thus be applied for evaluating the severity of joint OA and the treatment given to the patient.

关键词： osteoarthritis(OA) tribology synovial fluid(SF) pin-on-plate

QUADRATURE METHODS FOR HIGHLY OSCILLATORY SINGULAR INTEGRALS

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Journal of Computational Mathematics 2021年第2期39卷 227-260页

作者： Jing Gao Marissa Condon arieh Iserles Benjamin Gilvey Jon Trevelyan School of Mathematics and Statistics Xi'an Jiaotong UniversityXi'an 710049China School of Electronic Engineering Dublin City UniversityIreland DAMTP Centre for Mathematical SciencesUniversity of CambridgeUK Department of Engineering Durham UniversityUK

We address the evaluation of highly oscillatory integrals,with power-law and logarithmic *** problems arise in numerical methods in ***,the evaluation of oscillatory integrals dominates the run-time for wave-enriched boundary integral formulations for wave scattering,and many of these exhibit *** show that the asymptotic behaviour of the integral depends on the integrand and its derivatives at the singular point of the integrand,the stationary points and the endpoints of the integral.A truncated asymptotic expansion achieves an error that decays faster for increasing *** on the asymptotic analysis,a Filon-type method is constructed to approximate the *** an asymptotic expansion,the Filon method achieves high accuracy for both small and large ***-valued quadrature involves interpolation at the zeros of polynomials orthogonal to a complex weight *** results indicate that the complex-valued Gaussian quadrature achieves the highest accuracy when the three methods are ***,while it achieves higher accuracy for the same number of function evaluations,it requires signi cant additional cost of computation of orthogonal polynomials and their zeros.

关键词： Numerical quadrature Singular highly oscillatory integrals Asymptotic analysis Boundary Element Method Plane wave enrichment Partition of Unity

Does the eclipse limit bacterial nucleoid complexity and cell width?

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Synthetic and Systems Biotechnology 2017年第4期2卷 267-275页

作者： arieh Zaritsky Avinoam Rabinovitch Chenli Liu Conrad L.Woldringh Faculty of Natural Sciences Ben-Gurion University of the NegevPOB 653Be'er-Sheva84105Israel Center for Synthetic Biology Engineering Research Shenzhen Institutes of Advanced Technology(SIAT)Chinese Academy of SciencesShenzhenPR China Bacterial Cell Biology SILSBoelelaan 1108AmsterdamThe Netherlands

Cell size of bacteria M is related to 3 temporal parameters:chromosome replication time C,period from replication-termination to subsequent division D,and doubling time ***-state,bacillary cells grow exponentially by extending length L only,but their constant width W is larger at shorter t‘s or longer C's,in proportion to the number of chromosome replication positions n(?C/t),at least in Escherichia coli and Salmonella *** C by thymine limitation of fast-growing thyA mutants result in continuous increase of M,associated with rising W,up to a limit before branching.A set of such puzzling observations is qualitatively consistent with the view that the actual cell mass(or volume)at the time of replication-initiation Mi(or Vi),usually relatively constant in growth at varying t0s,rises with time under thymine limitation of fast-growing,thymine-requiring *** *** hypothesis will be tested that presumes existence of a minimal distance lmin between successive moving replisomes,translated into the time needed for a replisome to reach lmin before a newreplication-initiation at oriC is allowed,termed Eclipse *** analysis of currently available data is inconsistent with a constant E under all conditions,hence other explanations andways to test themare proposed in an attempt to elucidate these and other *** complex hypothesis takes into account much of what is currently known about Bacterial Physiology:the relationships between cell dimensions,growth and cycle parameters,particularly nucleoid structure,replication and position,and themode of peptidoglycan *** experiments arementioned that are necessary to test the discussed ideas and hypotheses.

关键词： Bacterial cell cycle Size and dimensions Growth Replication and division Nucleoid complexity Eclipse

A Short Note on Self-Similar Solution to Unconfined Flow in an Aquifer with Accretion

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Open Journal of Fluid Dynamics 2015年第1期5卷 51-57页

作者： arieh Pistiner Unit for Hydrocarbon Pollution Prevention Ministry of the Environmental Protection Haifa Israel

In this study we refer to a non-steady state, one-dimensional (on the x-axis), unconfined and saturated flow in an aquifer, described by the Boussinesq equation, combined with accretion. In accordance with the above, the moving boundary of the saturated area (toward x → +∝) serves as a horizontal water flux source to the unsaturated area. As time advances, the horizontally saturated zone, lying on the x-axis, becomes wider. A self-similar solution is derived that, after some mathematical manipulation, it is described in terms of Hypergeometric functions. The long-time behaviors of the solution describe the situation at which the water flux, that penetrates horizontally to the non-saturated zone, is equal to the water flux entering into the saturated zone.

关键词： Boussinesq Equation Self-Similar Solution Hypergeometric Function

The Rise and Fall of the Hydrophobic Effect in Protein Folding and Protein-Protein Association, and Molecular Recognition

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Open Journal of Biophysics 2011年第1期1卷 1-7页

作者： arieh Ben-Naim 不详

In the beginning everything was explained in Biochemistry in terms of hydrogen-bonds (HB). Then, the devastating blow, known as the HB-inventory argument came;hydrogen bonding with water molecules compete with intramolecular hydrogen-bonds. As a result, the HBs paradigm fell from grace. The void created was immediately filled by Kauzmann’s idea of hydrophobic (HφO) effect which reigned supreme in biochemical literature for over 50 years (1960-2010). Cracks in the HB-inventory argument on one hand, and doubts about the adequacy of Kauzmann’s model for the HφO effect, have led to a comeback of the HBs, along with a host of new hydrophilic (HφI) effects. The HφO effects lost much of its power - which it never really had - in explaining protein folding and protein-protein association. Instead, the more powerful and richer repertoire of HφI effects took over the reins. The interactions also offered simple and straightforward answers to the problems of protein folding, and protein-protein association.

关键词： Protein Folding Protein Association Molecular Recognition Hydrophobic Hydrophilic Interactions