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Article ; Online: Weighted ensemble: Recent mathematical developments.

Aristoff, D / Copperman, J / Simpson, G / Webber, R J / Zuckerman, D M

2023 Volume 158, Issue 1, Page(s) 14108

Abstract: Weighted ensemble (WE) is an enhanced sampling method based on periodically replicating and pruning trajectories generated in parallel. WE has grown increasingly popular for computational biochemistry problems due, in part, to improved hardware and ... ...

Abstract	Weighted ensemble (WE) is an enhanced sampling method based on periodically replicating and pruning trajectories generated in parallel. WE has grown increasingly popular for computational biochemistry problems due, in part, to improved hardware and accessible software implementations. Algorithmic and analytical improvements have played an important role, and progress has accelerated in recent years. Here, we discuss and elaborate on the WE method from a mathematical perspective, highlighting recent results that enhance the computational efficiency. The mathematical theory reveals a new strategy for optimizing trajectory management that approaches the best possible variance while generalizing to systems of arbitrary dimension.
MeSH term(s)	Algorithms ; Software
Language	English
Publishing date	2023-01-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0110873
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Book ; Online: Weighted ensemble

Aristoff, D. / Copperman, J. / Simpson, G. / Webber, R. J. / Zuckerman, D. M.

Recent mathematical developments

2022

Abstract: The weighted ensemble (WE) method, an enhanced sampling approach based on periodically replicating and pruning trajectories in a set of parallel simulations, has grown increasingly popular for computational biochemistry problems, due in part to improved ... ...

Abstract	The weighted ensemble (WE) method, an enhanced sampling approach based on periodically replicating and pruning trajectories in a set of parallel simulations, has grown increasingly popular for computational biochemistry problems, due in part to improved hardware and the availability of modern software. Algorithmic and analytical improvements have also played an important role, and progress has accelerated in recent years. Here, we discuss and elaborate on the WE method from a mathematical perspective, highlighting recent results which have begun to yield greater computational efficiency. Notable among these innovations are variance reduction approaches that optimize trajectory management for systems of arbitrary dimensionality. Comment: 12 pages, 10 figures
Keywords	Physics - Computational Physics ; Computer Science - Computational Engineering ; Finance ; and Science
Publishing date	2022-06-29
Publishing country	us
Document type	Book ; Online
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Article: The need to improve informed consent for breast cancer patients.

Zuckerman, D M

Journal of the American Medical Women's Association (1972)

2000 Volume 55, Issue 5, Page(s) 285–289

Abstract: Many of the more than 182,000 women who will be newly diagnosed with breast cancer this year will not have access to all the information they need to make the surgical and treatment choices that are most appropriate for them. Research clearly shows that ... ...

Abstract	Many of the more than 182,000 women who will be newly diagnosed with breast cancer this year will not have access to all the information they need to make the surgical and treatment choices that are most appropriate for them. Research clearly shows that lumpectomy and other breast-conserving surgeries are just as safe as mastectomy for most women with early stage disease, and yet approximately half will undergo the more disfiguring procedures. Choices about breast implants and autologous tissue reconstruction are based, at best, on a few published studies that provide limited information about the long-term safety of these procedures. Many healthy women who have strong family histories of breast cancer consider prophylactic mastectomies, and their decisions are also based on very limited information, because there are few studies showing the effectiveness of that procedure. This paper delineates how limited information and biased recommendations can undermine breast cancer patients' ability to make informed choices.
MeSH term(s)	Adult ; Breast Neoplasms/pathology ; Breast Neoplasms/prevention & control ; Breast Neoplasms/surgery ; Decision Making ; Female ; Humans ; Information Services ; Informed Consent ; Mastectomy ; Mastectomy, Segmental ; Physician-Patient Relations ; Reconstructive Surgical Procedures
Language	English
Publishing date	2000
Publishing country	United States
Document type	Journal Article
ZDB-ID	121272-2
ISSN	1551-8221 ; 0098-8421 ; 0091-7427
ISSN (online)	1551-8221
ISSN	0098-8421 ; 0091-7427
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Article: Media violence, gun control, and public policy.

Zuckerman, D M

The American journal of orthopsychiatry

1996 Volume 66, Issue 3, Page(s) 378–389

Abstract: Public concern with the national level of violence is discussed, and the complexity of the issue delineated. Research findings in two key areas of the topic, media violence and availability of firearms, are examined, as is their applicability to public ... ...

Abstract	Public concern with the national level of violence is discussed, and the complexity of the issue delineated. Research findings in two key areas of the topic, media violence and availability of firearms, are examined, as is their applicability to public policy efforts and recommendations for the prevention of violence. An approach that combines efforts to counteract media violence with those aimed at effective gun control is outlined in terms of bringing about changes in attitudes toward violence and firearm possession.
MeSH term(s)	Adolescent ; Adult ; Firearms/legislation & jurisprudence ; Humans ; Legislation as Topic ; Male ; Mass Media ; Middle Aged ; Public Policy ; Violence
Language	English
Publishing date	1996-07
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	280031-7
ISSN	1939-0025 ; 0002-9432
ISSN (online)	1939-0025
ISSN	0002-9432
DOI	10.1037/h0080188
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Article ; Online: Thermal motions of the E. coli glucose-galactose binding protein studied using well-sampled, semi-atomistic simulations.

Cashman, D J / Mamonov, A B / Bhatt, D / Zuckerman, D M

Current topics in medicinal chemistry

2010 Volume 11, Issue 2, Page(s) 211–220

Abstract: The E. coli glucose-galactose chemosensory receptor is a 309 residue, 32 kDa protein consisting of two distinct structural domains. We used two computational methods to examine the protein's thermal fluctuations, including both the large-scale ... ...

Abstract	The E. coli glucose-galactose chemosensory receptor is a 309 residue, 32 kDa protein consisting of two distinct structural domains. We used two computational methods to examine the protein's thermal fluctuations, including both the large-scale interdomain movements that contribute to the receptor's mechanism of action, as well as smaller-scale motions. We primarily employ extremely fast, "semi-atomistic" Library-Based Monte Carlo (LBMC) simulations, which include all backbone atoms but "implicit" side chains. Our results were compared with previous experiments and all-atom molecular dynamics (MD) simulation. Both LBMC and MD simulations were performed using both the apo and glucose-bound form of the protein, with LBMC exhibiting significantly larger fluctuations. The LBMC simulations are in general agreement with the disulfide trapping experiments of Careaga & Falke (J. Mol. Biol., 1992, Vol. 226, 1219-35), which indicate that distant residues in the crystal structure (i.e. beta carbons separated by 10 to 20 angstroms) form spontaneous transient contacts in solution. Our simulations illustrate several possible "mechanisms" (configurational pathways) for these fluctuations. We also observe several discrepancies between our calculations and experimental rate constants. Nevertheless, we believe that our semi-atomistic approach could be used to study fluctuations in other proteins, perhaps for ensemble docking or other analyses of protein flexibility in virtual screening studies.
MeSH term(s)	Amino Acids/metabolism ; Apoenzymes/chemistry ; Apoenzymes/metabolism ; Calcium-Binding Proteins/chemistry ; Calcium-Binding Proteins/metabolism ; Crystallography, X-Ray ; Differential Thermal Analysis ; Disulfides/chemistry ; Escherichia coli ; Galactose/metabolism ; Glucose/metabolism ; Holoenzymes/chemistry ; Holoenzymes/metabolism ; Models, Molecular ; Molecular Dynamics Simulation ; Monosaccharide Transport Proteins/chemistry ; Monosaccharide Transport Proteins/metabolism ; Periplasmic Binding Proteins/chemistry ; Periplasmic Binding Proteins/metabolism ; Protein Binding ; Protein Conformation
Chemical Substances	Amino Acids ; Apoenzymes ; Calcium-Binding Proteins ; Disulfides ; Holoenzymes ; Monosaccharide Transport Proteins ; Periplasmic Binding Proteins ; galactose-binding protein ; Glucose (IY9XDZ35W2) ; Galactose (X2RN3Q8DNE)
Language	English
Publishing date	2010-10-13
Publishing country	United Arab Emirates
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2064823-6
ISSN	1873-4294 ; 1568-0266
ISSN (online)	1873-4294
ISSN	1568-0266
DOI	10.2174/156802611794863607
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Article: Efficient dynamic importance sampling of rare events in one dimension.

Zuckerman, D M / Woolf, T B

Physical review. E, Statistical, nonlinear, and soft matter physics

2001 Volume 63, Issue 1 Pt 2, Page(s) 16702

Abstract: Exploiting stochastic path-integral theory, we obtain by simulation substantial gains in efficiency for the computation of reaction rates in one-dimensional, bistable, overdamped stochastic systems. Using a well-defined measure of efficiency, we compare ... ...

Abstract	Exploiting stochastic path-integral theory, we obtain by simulation substantial gains in efficiency for the computation of reaction rates in one-dimensional, bistable, overdamped stochastic systems. Using a well-defined measure of efficiency, we compare implementations of "dynamic importance sampling" (DIMS) methods to unbiased simulation. The best DIMS algorithms are shown to increase efficiency by factors of approximately 20 for a 5k(B)T barrier height and 300 for 9k(B)T, compared to unbiased simulation. The gains result from close emulation of natural (unbiased), instantonlike crossing events with artificially decreased waiting times between events that are corrected for in rate calculations. The artificial crossing events are generated using the closed-form solution to the most probable crossing event described by the Onsager-Machlup action. While the best biasing methods require the second derivative of the potential (resulting from the "Jacobian" term in the action, which is discussed at length), algorithms employing solely the first derivative do nearly as well. We discuss the importance of one-dimensional models to larger systems, and suggest extensions to higher-dimensional systems.
MeSH term(s)	Algorithms ; Computer Simulation ; Mathematical Computing ; Models, Theoretical ; Selection Bias ; Stochastic Processes
Language	English
Publishing date	2001-01
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, U.S. Gov't, P.H.S.
ISSN	1539-3755
ISSN	1539-3755
DOI	10.1103/PhysRevE.63.016702
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Book ; Online: Rapid sampling of all-atom peptides using a library-based polymer-growth approach

Mamonov, A. B. / Zhang, X. / Zuckerman, D. M.

2009

Abstract: We adapted existing polymer growth strategies for equilibrium sampling of peptides described by modern atomistic forcefields with implicit solvent. The main novel feature of our approach is the use of pre-calculated statistical libraries of molecular ... ...

Abstract	We adapted existing polymer growth strategies for equilibrium sampling of peptides described by modern atomistic forcefields with implicit solvent. The main novel feature of our approach is the use of pre-calculated statistical libraries of molecular fragments. A molecule is sampled by combining fragment configurations -- of single residues in this study -- which are stored in the libraries. Ensembles generated from the independent libraries are reweighted to conform with the Boltzmann factor distribution of the forcefield describing the full molecule. In this way, high-quality equilibrium sampling of small peptides (4-8 residues) typically requires less than one hour of single-processor wallclock time and can be significantly faster than Langevin simulations. Furthermore, approximate but clash-free ensembles can be generated for larger peptides (e.g., 16 residues) in less than a minute of single-processor computing. We also describe an application to free energy calculation, a "multi-resolution" implementation of the growth procedure and application to fragment assembly protein-structure prediction protocols.
Keywords	Physics - Biological Physics ; Physics - Computational Physics
Subject code	612
Publishing date	2009-10-13
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Asymmetric primitive-model electrolytes: Debye-Hückel theory, criticality, and energy bounds.

Zuckerman, D M / Fisher, M E / Bekiranov, S

Physical review. E, Statistical, nonlinear, and soft matter physics

2001 Volume 64, Issue 1 Pt 1, Page(s) 11206

Abstract: Debye-Hückel (DH) theory is extended to treat two-component size- and charge-asymmetric primitive models, focusing primarily on the 1:1 additive hard-sphere electrolyte with, say, negative ion diameters a(--) larger than the positive ion diameters a(++). ...

Abstract	Debye-Hückel (DH) theory is extended to treat two-component size- and charge-asymmetric primitive models, focusing primarily on the 1:1 additive hard-sphere electrolyte with, say, negative ion diameters a(--) larger than the positive ion diameters a(++). The treatment highlights the crucial importance of the charge-unbalanced "border zones" around each ion into which other ions of only one species may penetrate. Extensions of the DH approach that describe the border zones in a physically reasonable way are exact at high T and low density rho and, furthermore, are also in substantial agreement with recent simulation predictions for trends in the critical parameters, T(c) and rho(c), with increasing size asymmetry. Conversely, the simplest linear asymmetric DH description, which fails to account for physically expected behavior in the border zones at low T, can violate a new lower bound on the energy (which applies generally to models asymmetric in both charge and size). Other theories, including those based on the mean spherical approximation, predict trends in the critical parameters quite opposite to those established by the simulations.
MeSH term(s)	Biophysics/methods ; Diffusion ; Electrolytes ; Evaluation Studies as Topic ; Ions ; Mathematics ; Models, Chemical ; Models, Statistical ; Nonlinear Dynamics ; Solutions ; Static Electricity ; Thermodynamics
Chemical Substances	Electrolytes ; Ions ; Solutions
Language	English
Publishing date	2001-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
ISSN	1539-3755
ISSN	1539-3755
DOI	10.1103/PhysRevE.64.011206
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Article: Retrospective study of interests and abilities that predict life goals and sex-role attitudes of college women.

Zuckerman, D M

Psychological reports

1978 Volume 43, Issue 3 Pt 2, Page(s) 1151–1157

MeSH term(s)	Achievement ; Adult ; Attitude ; Female ; Gender Identity ; Goals ; Humans ; Identification (Psychology) ; Retrospective Studies ; Women
Language	English
Publishing date	1978-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	205658-6
ISSN	1558-691X ; 0033-2941
ISSN (online)	1558-691X
ISSN	0033-2941
DOI	10.2466/pr0.1978.43.3f.1151
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Article: Television's impact on children.

Zuckerman, D M / Zuckerman, B S

Pediatrics

1985 Volume 75, Issue 2, Page(s) 233–240

Abstract: Television has a major impact on children's knowledge, attitudes, and behavior. Research has demonstrated the association between television viewing and four areas: (1) children's aggressive behavior; (2) racial and sex-role stereotypes; (3) decreased ... ...

Abstract	Television has a major impact on children's knowledge, attitudes, and behavior. Research has demonstrated the association between television viewing and four areas: (1) children's aggressive behavior; (2) racial and sex-role stereotypes; (3) decreased interest in reading and school activities; and (4) poorer health habits and attitudes. Methodological limitations make it difficult to draw firm conclusions about a causal relationship between television viewing and children's behavior. Representative studies in these four areas are reviewed, important methodological concerns are pointed out, and conclusions from the research findings are drawn. The implications of the data for pediatricians and other health professionals are discussed.
MeSH term(s)	Advertising as Topic ; Attitude to Health ; Child ; Child Behavior ; Child, Preschool ; Feeding Behavior ; Humans ; Intelligence ; Interpersonal Relations ; Prejudice ; Reading ; Stereotyping ; Television ; Violence
Language	English
Publishing date	1985-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	207677-9
ISSN	1098-4275 ; 0031-4005
ISSN (online)	1098-4275
ISSN	0031-4005
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