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Michael W. Deem

Publications and source records attributed to Michael W. Deem.

At least 73 records · Page 4Linked to original sources
arXiv2003

Sequence Space Localization in the Immune System Response to Vaccination and Disease

We introduce a model of protein evolution to explain limitations in the immune system response to vaccination and disease. The phenomenon of original antigenic sin, wherein vaccination creates memory sequences that can \emph{increase} susceptibility to future exposures to the same disease, is explained as stemming from localization of the immune system response in antibody sequence space. This localization is a result of the roughness in sequence space of the evolved antibody affinity constant for antigen and is observed for diseases with high year-to-year mutation rates, such as influenza.

cond-mat.stat-mech↗
arXiv2003

A Statistical Theory of Isotropic Turbulence Well-Defined within the Context of the $ε$ Expansion

A new statistical field-theory model of isotropic turbulence is introduced. The model renormalizes the effects of turbulent stresses into a velocity-gradient-dependent random force. The model is well-defined within the context of the renormalization group $ε$ expansion, as the effective expansion parameter is $O(ε)$. The Kolmogorov constant and $N$ parameter of turbulence are of order unity, in accord with experimental results. Nontrivial intermittency corrections to the single-time structure functions are calculated as a controlled expansion in $ε$.

cond-mat.stat-mech↗
arXiv2002

Strategies for High-Throughput, Templated Zeolite Synthesis

How best to design and redesign high-throughput experiments for zeolite synthesis is addressed. A model that relates materials function to chemical composition of the zeolite and the structure directing agent is introduced. Using this model, several Monte Carlo-like design protocols are evaluated. Multi-round protocols are found to be effective, and strategies that use a priori information about the structure-directing libraries are found to be the best.

cond-mat.stat-mech↗
arXiv2002

Reaction, Levy Flights, and Quenched Disorder

We consider the A + A --> emptyset reaction, where the transport of the particles is given by Levy flights in a quenched random potential. With a common literature model of the disorder, the random potential can only increase the rate of reaction. With a model of the disorder that obeys detailed balance, however, the rate of reaction initially increases and then decreases as a function of the disorder strength. The physical behavior obtained with this second model is in accord with that for reactive turbulent flow, indicating that Levy flight statistics can model aspects of turbulent fluid transport.

cond-mat.stat-mech↗
arXiv2001

Monte Carlo Study of the Nucleation Process during Zeolite Synthesis

An atomic-scale model for silicate solutions is introduced for investigation of the nucleation process during zeolite synthesis in the absence of a structure directing agent. Monte Carlo schemes are developed to determine the equilibrium distribution of silicate cluster sizes within the context of this model. How the nucleation barrier and critical cluster size change with Si monomer concentration is discussed. Distance and angle histograms as well as ring size distributions are calculated and compared with known zeolite structures. The free energies of critical clusters are compared with those for small clusters of alpha-quartz.

cond-mat.stat-mech↗
arXiv2001

Dispersion Coefficients by a Field-Theoretic Renormalization of Fluid Mechanics

We consider subtle correlations in the scattering of fluid by randomly placed obstacles, which have been suggested to lead to a diverging dispersion coefficient at long times for high Peclet numbers, in contrast to finite mean-field predictions. We develop a new master equation description of the fluid mechanics that incorporates the physically relevant fluctuations, and we treat those fluctuations by a renormalization group procedure. We find a finite dispersion coefficient at low volume fraction of disorder and high Peclet numbers.

cond-mat.stat-mech↗
arXiv2001

Monte Carlo Methods for Small Molecule High-Throughput Experimentation

By analogy with Monte Carlo algorithms, we propose new strategies for design and redesign of small molecule libraries in high-throughput experimentation, or combinatorial chemistry. Several Monte Carlo methods are examined, including Metropolis, three types of biased schemes, and composite moves that include swapping or parallel tempering. Among them, the biased Monte Carlo schemes exhibit particularly high efficiency in locating optimal compounds. The Monte Carlo strategies are compared to a genetic algorithm approach. Although the best compounds identified by the genetic algorithm are comparable to those from the better Monte Carlo schemes, the diversity of favorable compounds identified is reduced by roughly 60%.

cond-mat.stat-mech↗
arXiv2000

A Statistical Mechanical Approach to Combinatorial Chemistry

An analogy between combinatorial chemistry and Monte Carlo computer simulation is pursued. Examples of how to design libraries for both materials discovery and protein molecular evolution are given. For materials discovery, the concept of library redesign, or the use previous experiments to guide the design of new experiments, is introduced. For molecular evolution, examples of how to use ``biased'' Monte Carlo to search the protein sequence space are given. Chemical information, whether intuition, theoretical calculations, or database statistics, can be naturally incorporated as an a priori bias in the Monte Carlo approach to library design in combinatorial chemistry. In this sense, combinatorial chemistry can be viewed as an extension of traditional chemical synthesis.

cond-mat.stat-mech↗
arXiv2000

Library Design in Combinatorial Chemistry by Monte Carlo Methods

Strategies for searching the space of variables in combinatorial chemistry experiments are presented, and a random energy model of combinatorial chemistry experiments is introduced. The search strategies, derived by analogy with the computer modeling technique of Monte Carlo, effectively search the variable space even in combinatorial chemistry experiments of modest size. Efficient implementations of the library design and redesign strategies are feasible with current experimental capabilities.

cond-mat.stat-mech↗
arXiv2000

Disorder-Induced Time-Dependent Diffusion in Zeolites

We suggest that disordered framework aluminums and non-framework cations can create a disordered electrostatic potential in zeolites that can lead to a discrepancy between diffusivities measured by microscopic and macroscopic experimental techniques. We calculate the value of the discrepancy and the characteristic time scale at which it occurs for several ionic and polarizable species diffusing in zeolites. For ionic species, a discrepancy is almost inevitable. For polarizable species, a significant discrepancy may occur in some zeolites only for long alkanes or large species such as benzene.

cond-mat.stat-mech↗
arXiv1999

DNA transport by a micromachined Brownian ratchet device

We have micromachined a silicon-chip device that transports DNA with a Brownian ratchet that rectifies the Brownian motion of microscopic particles. Transport properties for a DNA 50mer agree with theoretical predictions, and the DNA diffusion constant agrees with previous experiments. This type of micromachine could provide a generic pump or separation component for DNA or other charged species as part of a microscale lab-on-a-chip. A device with reduced feature size could produce a size-based separation of DNA molecules, with applications including the detection of single nucleotide polymorphisms.

physics.bio-ph↗
arXiv1999

Analytical Rebridging Monte Carlo: Application to cis/trans Isomerization in Proline-Containing, Cyclic Peptides

We present a new method, the analytical rebridging scheme, for Monte Carlo simulation of proline-containing, cyclic peptides. The cis/trans isomerization is accommodated by allowing for two states of the amide bond. We apply our method to five peptides that have been previously characterized by NMR methods. Our simulations achieve effective equilibration and agree well with experimental data in all cases. We discuss the importance of effective equilibration and the role of bond flexibility and solvent effects on the predicted equilibrium properties.

physics.chem-ph↗
arXiv1999

Efficient Monte Carlo Methods for Cyclic Peptides

We present a new, biased Monte Carlo scheme for simulating complex, cyclic peptides. Backbone atoms are equilibrated with a biased rebridging scheme, and side-chain atoms are equilibrated with a look-ahead configurational bias Monte Carlo. Parallel tempering is shown to be an important ingredient in the construction of an efficient approach.

physics.bio-ph↗
arXiv1999

A Hierarchical Approach to Protein Molecular Evolution

Biological diversity has evolved despite the essentially infinite complexity of protein sequence space. We present a hierarchical approach to the efficient searching of this space and quantify the evolutionary potential of our approach with Monte Carlo simulations. These simulations demonstrate that non-homologous juxtaposition of encoded structure is the rate-limiting step in the production of new tertiary protein folds. Non-homologous ``swapping'' of low energy secondary structures increased the binding constant of a simulated protein by $\approx10^7$ relative to base substitution alone. Applications of our approach include the generation of new protein folds and modeling the molecular evolution of disease.

cond-mat.stat-mech↗
arXiv1998

Field Theoretic Approach to Long Range Reactions

We analyze bimolecular reactions that proceed by a long-ranged reactive interaction, using a field theoretic approach that takes into account fluctuations. We consider both the one-species, $A+A \to \emptyset$ reaction and the two-species, $A+B \to \emptyset$ reaction. We consider both mobile and immobile reactants, both in the presence and in the absence of adsorption.

cond-mat.stat-mech↗
arXiv1998

``Superfast'' Reaction in Turbulent Flow with Potential Disorder

We explore the regime of ``superfast'' reactivity that has been predicted to occur in turbulent flow in the presence of potential disorder. Computer simulation studies confirm qualitative features of the previous renormalization group predictions, which were based on a static model of turbulence. New renormalization group calculations for a more realistic, dynamic model of turbulence show that the superfast regime persists. This regime, with concentration decay exponents greater than that for a well-mixed reaction, appears to be a general result of the interplay among non-linear reaction kinetics, turbulent transport, and local trapping by potential disorder.

cond-mat.stat-mech↗
arXiv1998

Strict Detailed Balance is Unnecessary in Monte Carlo Simulation

Detailed balance is an overly strict condition to ensure a valid Monte Carlo simulation. We show that, under fairly general assumptions, a Monte Carlo simulation need satisfy only the weaker balance condition. Not only does our proof show that sequential updating schemes are correct, but also it establishes the correctness of a whole class of new methods that simply leave the Boltzmann distribution invariant.

cond-mat.stat-mech↗