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Dive into the research topics where Manan Chopra is active.

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Featured researches published by Manan Chopra.


Journal of Chemical Physics | 2005

Optimal allocation of replicas in parallel tempering simulations

Nitin Rathore; Manan Chopra; Juan J. de Pablo

We have studied the efficiency of parallel tempering simulations for a variety of systems including a coarse-grained protein, an atomistic model polypeptide, and the Lennard-Jones fluid. A scheme is proposed for the optimal allocation of temperatures in these simulations. The method is compared to the existing empirical approaches used for this purpose. Accuracy associated with the computed thermodynamic quantities such as specific heat is also computed and their dependence on the trial-exchange acceptance rate is reported.


Biophysical Journal | 2010

Solution Structures of Rat Amylin Peptide: Simulation, Theory, and Experiment

Allam S. Reddy; Lu Wang; Yu-Shan Lin; Yun Ling; Manan Chopra; Martin T. Zanni; J. L. Skinner; Juan J. de Pablo

Amyloid deposits of amylin in the pancreas are an important characteristic feature found in patients with Type-2 diabetes. The aggregate has been considered important in the disease pathology and has been studied extensively. However, the secondary structures of the individual peptide have not been clearly identified. In this work, we present detailed solution structures of rat amylin using a combination of Monte Carlo and molecular dynamics simulations. A new Monte Carlo method is presented to determine the free energy of distinct biomolecular conformations. Both folded and random-coil conformations of rat amylin are observed in water and their relative stability is examined in detail. The former contains an alpha-helical segment comprised of residues 7-17. We find that at room temperature the folded structure is more stable, whereas at higher temperatures the random-coil structure predominates. From the configurations and weights we calculate the alpha-carbon NMR chemical shifts, with results that are in reasonable agreement with experiments of others. We also calculate the infrared spectrum in the amide I stretch regime, and the results are in fair agreement with the experimental line shape presented herein.


Annual Review of Chemical and Biomolecular Engineering | 2012

Density of States–Based Molecular Simulations

Sadanand Singh; Manan Chopra; Juan J. de Pablo

One of the central problems in statistical mechanics is that of finding the density of states of a system. Knowledge of the density of states of a system is equivalent to knowledge of its fundamental equation, from which all thermodynamic quantities can be obtained. Over the past several years molecular simulations have made considerable strides in their ability to determine the density of states of complex fluids and materials. In this review we discuss some of the more promising approaches proposed in the recent literature along with their advantages and limitations.


Journal of Chemical Physics | 2006

Order-parameter-based Monte Carlo simulation of crystallization

Manan Chopra; Marcus Müller; J. J. de Pablo

A Monte Carlo simulation method is presented for simulation of phase transitions, with emphasis on the study of crystallization. The method relies on a random walk in order parameter Phi(q(N)) space to calculate a free energy profile between the two coexisting phases. The energy and volume data generated over the course of the simulation are subsequently reweighed to identify the precise conditions for phase coexistence. The usefulness of the method is demonstrated in the context of crystallization of a purely repulsive Lennard-Jones system. A systematic analysis of precritical and critical nuclei as a function of supercooling reveals a gradual change from a bcc to a fcc structure inside the crystalline nucleus as it grows at large degrees of supercooling. The method is generally applicable and is expected to find applications in systems for which two or more coexisting phases can be distinguished through one or more order parameters.


Biophysical Journal | 2010

GNNQQNY—Investigation of Early Steps during Amyloid Formation

Allam S. Reddy; Manan Chopra; Juan J. de Pablo

Protein aggregation has been implicated in the pathology of several neurodegenerative diseases, and a better understanding of how it proceeds is essential for the development of therapeutic strategies. Recently, the amyloidogenic heptapeptide GNNQQNY has emerged as a molecule of choice for fundamental studies of protein aggregation. A number of experimental and computational studies have examined the structure of the GNNQQNY aggregate. Less work, however, has been aimed at understanding its aggregation pathway. In this study, we present a detailed computational analysis of such a pathway. To that end, transition path sampling Monte Carlo simulations are used to examine the dimerization process. A statistical analysis of the reaction pathways shows that the dimerization reaction proceeds via a zipping mechanism, initiated with the formation of distinct contacts at the third residue (N). Asparagine residues are found to play a key role in the early stages of aggregation. And, contrary to previous belief, it is also shown that the tyrosine terminal group is not required to stabilize the dimer. In fact, an asparagine residue leads to faster aggregation of the peptide.


Journal of Chemical Physics | 2008

Folding of polyglutamine chains

Manan Chopra; Allam S. Reddy; Nicholas L. Abbott; J. J. de Pablo

Long polyglutamine chains have been associated with a number of neurodegenerative diseases. These include Huntingtons disease, where expanded polyglutamine (PolyQ) sequences longer than 36 residues are correlated with the onset of symptoms. In this paper we study the folding pathway of a 54-residue PolyQ chain into a beta-helical structure. Transition path sampling Monte Carlo simulations are used to generate unbiased reactive pathways between unfolded configurations and the folded beta-helical structure of the polyglutamine chain. The folding process is examined in both explicit water and an implicit solvent. Both models reveal that the formation of a few critical contacts is necessary and sufficient for the molecule to fold. Once the primary contacts are formed, the fate of the protein is sealed and it is largely committed to fold. We find that, consistent with emerging hypotheses about PolyQ aggregation, a stable beta-helical structure could serve as the nucleus for subsequent polymerization of amyloid fibrils. Our results indicate that PolyQ sequences shorter than 36 residues cannot form that nucleus, and it is also shown that specific mutations inferred from an analysis of the simulated folding pathway exacerbate its stability.


Journal of Chemical Physics | 2009

Hydrodynamic effects on the translocation rate of a polymer through a pore.

Juan P. Hernández-Ortiz; Manan Chopra; Stephanie Geier; Juan J. de Pablo

The translocation of large DNA molecules through narrow pores has been examined in the context of multiscale simulations that include a full coupling of fluctuating hydrodynamic interactions, boundary effects, and molecular conformation. The actual rate constants for this process are determined for the first time, and it is shown that hydrodynamic interactions can lead to translocation rates that vary by multiple orders of magnitude when molecular weights are only changed by a factor of 10, in stark contrast to predictions from widely used free draining calculations.


Journal of Chemical Physics | 2008

Improved transition path sampling methods for simulation of rare events

Manan Chopra; Rohit Malshe; Allam S. Reddy; J. J. de Pablo

The free energy surfaces of a wide variety of systems encountered in physics, chemistry, and biology are characterized by the existence of deep minima separated by numerous barriers. One of the central aims of recent research in computational chemistry and physics has been to determine how transitions occur between deep local minima on rugged free energy landscapes, and transition path sampling (TPS) Monte-Carlo methods have emerged as an effective means for numerical investigation of such transitions. Many of the shortcomings of TPS-like approaches generally stem from their high computational demands. Two new algorithms are presented in this work that improve the efficiency of TPS simulations. The first algorithm uses biased shooting moves to render the sampling of reactive trajectories more efficient. The second algorithm is shown to substantially improve the accuracy of the transition state ensemble by introducing a subset of local transition path simulations in the transition state. The system considered in this work consists of a two-dimensional rough energy surface that is representative of numerous systems encountered in applications. When taken together, these algorithms provide gains in efficiency of over two orders of magnitude when compared to traditional TPS simulations.


Journal of Chemical Physics | 2006

Improved density of states Monte Carlo method based on recycling of rejected states

Manan Chopra; J. J. de Pablo

In this paper a new algorithm is presented that improves the efficiency of Wang and Landau algorithm or density of states (DOS) Monte Carlo simulations by employing rejected states. The algorithm is shown to have a performance superior to that of the original Wang-Landau [F. Wang and D. P. Landau, Phys. Rev. Lett. 86, 2050 (2001)] algorithm and the more recent configurational temperature DOS algorithm. The performance of the method is illustrated in the context of results for the Lennard-Jones fluid.


Biophysical Journal | 2005

Interactions of liquid crystal-forming molecules with phospholipid bilayers studied by molecular dynamics simulations.

Nathan A. Lockwood; Manan Chopra; Orlando Guzmán; Nicholas L. Abbott; Juan J. de Pablo

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Allam S. Reddy

University of Wisconsin-Madison

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J. J. de Pablo

University of Wisconsin-Madison

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Nicholas L. Abbott

University of Wisconsin-Madison

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Sadanand Singh

University of Wisconsin-Madison

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Orlando Guzmán

Universidad Autónoma Metropolitana

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J. L. Skinner

University of Wisconsin-Madison

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Lu Wang

University of Wisconsin-Madison

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Martin T. Zanni

University of Wisconsin-Madison

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Nathan A. Lockwood

University of Wisconsin-Madison

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