Sandipan Mohanty
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View article: Folding lattice proteins confined on minimal grids using a quantum-inspired encoding
Folding lattice proteins confined on minimal grids using a quantum-inspired encoding Open
Steric clashes pose a challenge when exploring dense protein systems using conventional explicit-chain methods. A minimal example is a single lattice protein confined on a minimal grid, with no free sites. Finding its minimum energy is a h…
View article: Ground state properties of a spin-$\frac{5}{2}$ frustrated triangular lattice antiferromagnet NH$_{4}$Fe(PO$_{3}$F)$_2$
Ground state properties of a spin-$\frac{5}{2}$ frustrated triangular lattice antiferromagnet NH$_{4}$Fe(PO$_{3}$F)$_2$ Open
Structural and magnetic properties of a two-dimensional spin-$\frac{5}{2}$ frustrated triangular lattice antiferromagnet NH$_{4}$Fe(PO$_{3}$F)$_2$ are explored via x-ray diffraction, magnetic susceptibility, high-field magnetization, heat …
View article: Evidence of quantum spin liquid state in a <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msup><mml:mrow><mml:mi>Cu</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn><mml:mo>+</mml:mo></mml:mrow></mml:msup></mml:math>-based <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>S</mml:mi><mml:mo>=</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mn>2</mml:mn></mml:mfrac></mml:mrow></mml:math> triangular lattice antiferromagnet
Evidence of quantum spin liquid state in a -based triangular lattice antiferromagnet Open
The layered triangular lattice owing to $1:2$ order of $B$ and $B'$ sites in\nthe triple perovskite $A_3 B B'_2$O$_9$ family provides an enticing domain for\nexploring the complex phenomena of quantum spin liquids (QSLs). We report a\ncomp…
View article: Using quantum annealing to design lattice proteins
Using quantum annealing to design lattice proteins Open
Quantum annealing has shown promise for finding solutions to difficult optimization problems, including protein folding. Recently, we used the D-Wave Advantage quantum annealer to explore the folding problem in a coarse-grained lattice mod…
View article: Folding lattice proteins with quantum annealing
Folding lattice proteins with quantum annealing Open
Quantum annealing is a promising approach for obtaining good approximate solutions to difficult optimization problems. Folding a protein sequence into its minimum-energy structure represents such a problem. For testing new algorithms and t…
View article: Limitations of field-theory simulation for exploring phase separation: The role of repulsion in a lattice protein model
Limitations of field-theory simulation for exploring phase separation: The role of repulsion in a lattice protein model Open
Field-theory simulation by the complex Langevin method offers an alternative to conventional sampling techniques for exploring the forces driving biomolecular liquid–liquid phase separation. Such simulations have recently been used to stud…
View article: When a foreign gene meets its native counterpart: computational biophysics analysis of two PgiC loci in the grass Festuca ovina
When a foreign gene meets its native counterpart: computational biophysics analysis of two PgiC loci in the grass Festuca ovina Open
Duplicative horizontal gene transfer may bring two previously separated homologous genes together, which may raise questions about the interplay between the gene products. One such gene pair is the “native” PgiC1 and “foreign” PgiC2 in the…
View article: High performance scientific computing in C
High performance scientific computing in C Open
View article: Protein folding/unfolding in the presence of interacting macromolecular crowders
Protein folding/unfolding in the presence of interacting macromolecular crowders Open
\nRecent years have seen an increasing number of biophysical studies of proteins being conducted in cells and concentrated protein solutions. In these experiments, compared to dilute-solution data, both stabilization and destabilization of…
View article: Erratum: “Equilibrium simulation of trp-cage in the presence of protein crowders” [J. Chem. Phys. 143, 175102 (2015)]
Erratum: “Equilibrium simulation of trp-cage in the presence of protein crowders” [J. Chem. Phys. 143, 175102 (2015)] Open
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View article: CECAM Tutorial - Atomistic Monte Carlo Simulation
CECAM Tutorial - Atomistic Monte Carlo Simulation Open
View article: Equilibrium simulation of trp-cage in the presence of protein crowders
Equilibrium simulation of trp-cage in the presence of protein crowders Open
While steric crowders tend to stabilize globular proteins, it has been found that protein crowders can have an either stabilizing or destabilizing effect, where a destabilization may arise from nonspecific attractive interactions between t…
View article: The Mont-Blanc Project: First Phase Successfully Finished
The Mont-Blanc Project: First Phase Successfully Finished Open
Running from October 2011 to June 2015, the aim of the European project Mont-Blanc has been to develop an approach to Exascale computing based on embedded power-efficient technology. The main goals of the project were to i) build an HPC pr…