Advances in Chemical Physics最新文献

{"title":"Local Fluctuations in Solution: Theory and Applications.","authors":"Elizabeth A Ploetz, Paul E Smith","doi":"10.1002/9781118571767.ch4","DOIUrl":"https://doi.org/10.1002/9781118571767.ch4","url":null,"abstract":"","PeriodicalId":50874,"journal":{"name":"Advances in Chemical Physics","volume":"153 ","pages":"311-372"},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/9781118571767.ch4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32220735","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Kinetics and Thermodynamics of Fluctuation‐Induced Transitions in Multistable Systems","authors":"G. Nicolis, C. Nicolis","doi":"10.1002/9781118309513.CH1","DOIUrl":"https://doi.org/10.1002/9781118309513.CH1","url":null,"abstract":"1 Kinetics and Thermodynamics of Fluctuation-Induced Transitions in Multistable Systems By Gregoire Nicolis and Catherine Nicolis 27 Dynamical Rare Event Simulation Techniques for Equilibrium and Nonequilibrium Systems By Titus S. Van Erp 61 Confocal Depolarized Dynamic Light Scattering By M. Potenza, T. Sanvito, V. Degiorgio, and M. Giglio 79 The Two-Step Mechanism and The Solution-Crystal Spinodal for Nucleation of Crystals in Solution By Peter G. Vekilov 111 Experimental Studies of Two-Step Nucleation During Two-Dimensional Crystallization of Colloidal Particles with Short-Range Attraction By John R. Savage, Liquan Pei, and Anthony D. Dinsmore 137 On the Role of Metastable Intermediate States in the Homogeneous Nucleation of Solids from Solution By James F. Lutsko 173 Effects of Protein Size on the High-Concentration/Low-Concentration Phase Transition By Patrick Grosfils 193 Geometric Constraints in the Self-Assembly of Mineral Dendrites and Platelets By John J. Kozak 223 What can Mesoscopic Level IN SITU Observations Teach us About Kinetics and Thermodynamics of Protein Crystallization? By Mike Sleutel, Dominique Maes, and Alexander Van Driessche","PeriodicalId":50874,"journal":{"name":"Advances in Chemical Physics","volume":"28 14","pages":"1-26"},"PeriodicalIF":0.0,"publicationDate":"2012-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50708073","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of Protein Size on the High‐Concentration/Low‐Concentration Phase Transition","authors":"P. Grosfils","doi":"10.1002/9781118309513.CH7","DOIUrl":"https://doi.org/10.1002/9781118309513.CH7","url":null,"abstract":"","PeriodicalId":50874,"journal":{"name":"Advances in Chemical Physics","volume":"27 15","pages":"173-191"},"PeriodicalIF":0.0,"publicationDate":"2012-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50707656","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Introduction to Quantum Algorithms for Physics and Chemistry","authors":"M. Yung, J. Whitfield, S. Boixo, D. G. Tempel, A. Aspuru‐Guzik","doi":"10.1002/9781118742631.ch03","DOIUrl":"https://doi.org/10.1002/9781118742631.ch03","url":null,"abstract":"An enormous number of model chemistries are used in computational chemistry to solve or approximately solve the Schrodinger equation; each with their own drawbacks. One key limitation is that the hardware used in computational chemistry is based on classical physics, and is often not well suited for simulating models in quantum physics. In this review, we focus on applications of quantum computation to chemical physics problems. We describe the algorithms that have been proposed for the electronic- structure problem, the simulation of chemical dynamics, thermal state preparation, density functional theory and adiabatic quantum simulation.","PeriodicalId":50874,"journal":{"name":"Advances in Chemical Physics","volume":"226 ","pages":"67-106"},"PeriodicalIF":0.0,"publicationDate":"2012-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/9781118742631.ch03","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50725259","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantum Dynamical Resonances in Chemical Reactions: From A + BC to Polyatomic Systems","authors":"Kopin Liu","doi":"10.1002/9781118180396.CH1","DOIUrl":"https://doi.org/10.1002/9781118180396.CH1","url":null,"abstract":"","PeriodicalId":50874,"journal":{"name":"Advances in Chemical Physics","volume":"187 3","pages":"1-46"},"PeriodicalIF":0.0,"publicationDate":"2012-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/9781118180396.CH1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50705768","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Determination of molecular orientational correlations in disordered systems from diffraction data","authors":"S. Pothoczki, L. Temleitner, L. Pusztai","doi":"10.1002/9781118197714.CH3","DOIUrl":"https://doi.org/10.1002/9781118197714.CH3","url":null,"abstract":"","PeriodicalId":50874,"journal":{"name":"Advances in Chemical Physics","volume":"96 1","pages":"143-168"},"PeriodicalIF":0.0,"publicationDate":"2012-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/9781118197714.CH3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50706141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Recent advances in studying mechanical properties of DNA","authors":"Reza Vafabakhsh, Kyung-Sun Lee, T. Ha","doi":"10.1002/9781118197714.CH4","DOIUrl":"https://doi.org/10.1002/9781118197714.CH4","url":null,"abstract":"","PeriodicalId":50874,"journal":{"name":"Advances in Chemical Physics","volume":"80 1","pages":"169-186"},"PeriodicalIF":0.0,"publicationDate":"2012-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/9781118197714.CH4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50706273","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Efficient and Unbiased Sampling of Biomolecular Systems in the Canonical Ensemble: A Review of Self-Guided Langevin Dynamics.","authors":"Xiongwu Wu, Ana Damjanovic, Bernard R Brooks","doi":"10.1002/9781118197714.ch6","DOIUrl":"10.1002/9781118197714.ch6","url":null,"abstract":"<p><p>This review provides a comprehensive description of the self-guided Langevin dynamics (SGLD) and the self-guided molecular dynamics (SGMD) methods and their applications. Example systems are included to provide guidance on optimal application of these methods in simulation studies. SGMD/SGLD has enhanced ability to overcome energy barriers and accelerate rare events to affordable time scales. It has been demonstrated that with moderate parameters, SGLD can routinely cross energy barriers of 20 kT at a rate that molecular dynamics (MD) or Langevin dynamics (LD) crosses 10 kT barriers. The core of these methods is the use of local averages of forces and momenta in a direct manner that can preserve the canonical ensemble. The use of such local averages results in methods where low frequency motion \"borrows\" energy from high frequency degrees of freedom when a barrier is approached and then returns that excess energy after a barrier is crossed. This self-guiding effect also results in an accelerated diffusion to enhance conformational sampling efficiency. The resulting ensemble with SGLD deviates in a small way from the canonical ensemble, and that deviation can be corrected with either an on-the-fly or a post processing reweighting procedure that provides an excellent canonical ensemble for systems with a limited number of accelerated degrees of freedom. Since reweighting procedures are generally not size extensive, a newer method, SGLDfp, uses local averages of both momenta and forces to preserve the ensemble without reweighting. The SGLDfp approach is size extensive and can be used to accelerate low frequency motion in large systems, or in systems with explicit solvent where solvent diffusion is also to be enhanced. Since these methods are direct and straightforward, they can be used in conjunction with many other sampling methods or free energy methods by simply replacing the integration of degrees of freedom that are normally sampled by MD or LD.</p>","PeriodicalId":50874,"journal":{"name":"Advances in Chemical Physics","volume":"150 ","pages":"255-326"},"PeriodicalIF":0.0,"publicationDate":"2012-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3731171/pdf/nihms412884.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31631734","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computational Studies of the Properties of DNA‐Linked Nanomaterials","authors":"One-Sun Lee, G. Schatz","doi":"10.1002/9781118180396.CH5","DOIUrl":"https://doi.org/10.1002/9781118180396.CH5","url":null,"abstract":"","PeriodicalId":50874,"journal":{"name":"Advances in Chemical Physics","volume":"148 ","pages":"197-249"},"PeriodicalIF":0.0,"publicationDate":"2012-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50706503","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Change‐Point Localization and Wavelet Spectral Analysis of Single‐Molecule Time Series","authors":"Haw Yang","doi":"10.1002/9781118131374.CH9","DOIUrl":"https://doi.org/10.1002/9781118131374.CH9","url":null,"abstract":"","PeriodicalId":50874,"journal":{"name":"Advances in Chemical Physics","volume":"38 1","pages":"217-243"},"PeriodicalIF":0.0,"publicationDate":"2011-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50705389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}