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Amylose and cellulose are important biopolymers with diverse applications in biotechnology and materials science. Understanding their structural, dynamic, and solvation properties at the molecular level is critical for harnessing their potential. This study investigates the electronic and structural properties of single-chain cellulose and single- and double-chain amylose in aqueous solution using molecular dynamics simulations with both nonpolarizable (CHARMM) and polarizable (Drude) force fields. CHARMM simulations show stable hydrogen bonding between amylose and water, higher glucose ring dipole moments, increased rigidity, adoption of chair conformations, and less variation in dihedral angles. In contrast, Drude simulations captured dynamic electronic polarization, enhanced conformational flexibility, and resulted in heterogeneous inter- and intramolecular hydrogen bonds. For cellulose, structural and solvation behaviors were largely similar between CHARMM and Drude. These findings highlight molecular interactions and solvation dynamics of amylose and cellulose, with potential relevance in materials science and biotechnology.

Dr. Ardem Patapoutian says he watches “with deep sadness as the United States’ remarkable scientific enterprise, which took generations of hard work and national investment to build, faces a concerted...

Computational simulations of biomolecules provide a wealth of information about the thermodynamic landscape of biologically important systems, kinetics of important cellular processes, and the biophys...

Contribute to Lemkul-Lab/gamd_livecoms_tutorial development by creating an account on GitHub.

We present the NetSci program–an open-source scientific software package designed for estimating mutual information (MI) between data sets using GPU acceleration and a k-nearest-neighbor algorithm. This approach significantly enhances calculation speed, achieving improvements of several orders of magnitude over traditional CPU-based methods, with data set size limits dictated only by available hardware. To validate NetSci, we accurately compute MI for an analytically verifiable two-dimensional Gaussian distribution and replicate the generalized correlation (GC) analysis previously conducted on the B1 domain of protein G. We also apply NetSci to molecular dynamics simulations of the Sarcoendoplasmic Reticulum Calcium-ATPase (SERCA) pump, exploring the allosteric mechanisms and pathways influenced by ATP and 2′-deoxy-ATP (dATP) binding. Our analysis reveals distinct allosteric effects induced by ATP compared to dATP, with predicted information pathways from the bound nucleotide to the calcium-binding domain differing based on the nucleotide involved. NetSci proves to be a valuable tool for estimating MI and GC in various data sets and is particularly effective for analyzing intraprotein communication and information transfer.

The environmental and economic challenges posed by the widespread use and disposal of plastics, particularly poly(ethylene terephthalate) (PET), require innovative solutions to mitigate their impact. ...

Since its inception nearly a half century ago, CHARMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and adva...

The environmental and economic challenges posed by the widespread use and disposal of plastics, particularly polyethylene terephthalate (PET), require innovative solutions to mitigate their impact. Su...

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The formation of G-quadruplexes (GQs) occurs in guanine-rich sequences of DNA and RNA, producing highly stable and structurally diverse noncanonical nucleic acid structures. GQs play crucial roles in ...

The tiny crystals, only a few nanometres in size, have applications in computing, lasers and microscopy