Fred

Abstract submissions for the 2nd Next-Gen Conversation open in less than a month.
We look forward to having you join us for a week of biomolecular structure and dynamics. Join us in Ruston, LA, in June 2026. t.co/H8FM4xuPTa

NIH will only accept six applications per PI per calendar year. NIH has issued NOT-OD-25-132 Supporting Fairness and Originality in NIH Research Applications which informs us that NIH will only accept six new, renewal, resubmission, or revision applications fro…

NIH will only accept six applications per PI per calendar year. drugmonkey.wordpress.com/2025/07/17/n...

Congrats to Dr. Corak for passing his defense !

PhD Defense - Nick Corak- Drought, Fire, and Vegetation Stress: Quantifying Ecosystem Responses to Extreme Events

Nick Corak, a Physics student in Dr. Lowman's group, will defend his dissertation this Thursday at 3:00 pm at Wake Downtown. Come on down! events.wfu.edu/event/phd-de...

If interested, let me know (salsbufr@wfu.edu) with your CV. These positions would be especially appropriate for mid-career faculty. 4/4 #JBSD

Structural Biology: expertise for submissions using Cryo-EM, X-ray crystallography, NMR, and hybrid methods combining multiple structural techniques, and/or integrated methods with computation. But their focus would be on experimental work. 3/4 #JBSD

Experimental Nucleic Acid Structure & Dynamics: expertise for submissions dealing with nucleic acid stability, thermodynamics, and folding dynamics; including uses of calorimetry, and fluorescence to study DNA/RNA interactions, nucleic acid binding, and structural stability. 2/4 #JBSD

The Journal of Biomolecular Structure & Dynamics is looking for more Associate Editors as we expand the scope of articles we attract. We are looking for experimentalists in 1) nucleic acid structure & dynamics and 2) Structural biology. More details in thread 1/4 #JBSD

Building Better Thinkers: Why STEM Minds Need a Palette of Liberal Arts Podcast Episode · Deacs.AI · 06/17/2025 · 58m

Check out me being interviewed on using AI in STEM education )yes my name is misspelled) podcasts.apple.com/us/podcast/d...

Funding opportunities in the NIH Guide! First time since late Jan I believe. grants.nih.gov/grants/guide...

Structural and accessibility studies highlight the differential binding of clemizole to TRPC5 and TRPC6 Transient Receptor Potential Canonical 5 (T RP C5) and T RP C6 channels play critical physiological roles in various cell types. Their involvement in numerous disease progression mechanisms has led...

Docking & in-silico mutagenesis show clemizole binds TRPC5 more tightly than TRPC6 because pocket residues in TRPC5 have higher ASA/RASA (greater accessibility). Accessibility is a key lever for designing selective TRPC inhibitors. #JBSD www.tandfonline.com/doi/full/10....

Antimicrobial peptide interactions with bacterial cell membranes Antimicrobial peptides (AMPs) are potential alternatives for common antibiotics because of their greater activity and efficiency against a broad range of viruses, bacteria, fungi, and parasites. In...

MD reveals how α-helical magainin-2 & β-sheet protegrin-1 target bacterial membranes. Electrostatic Lys/Arg contacts anchor peptides; ΔG favors protegrin-1 on POPG/POPE 3:1 and magainin-2 on POPG/POPE 1:3. Insights might help guide AMP design. #JBSD www.tandfonline.com/doi/full/10....

HrpY protein of Ralstonia solanacearum exhibits spontaneous formation of pilus like assembly: analysis of its stability Type 3 secretory system (T3SS), a complex protein machinery has a unique virulence mechanism that involves injecting effector proteins directly into host cells. The T3SS effector proteins are trans...

Recombinant HrpY from Ralstonia solanacearum self-assembles into pilus-like tubes (86–167 nm long, ~6 nm wide). Oligomers shrug off urea/GdnHCl & 50 °C but disassemble with detergents; SDS disrupts secondary structure. New clues to T3SS needle stability. #JBSD www.tandfonline.com/doi/full/10....

Switchable tetraplex elements in the heterogeneous nuclear ribonucleoprotein K promoter: micro-environment dictated structural transitions of G/C rich elements We have elucidated the hnRNP K promoter as a hotspot for tetraplex-based molecular switches receptive to micro-environmental stimuli. We have characterised the structural features of four tetraplex...

G/C-rich loci in the hnRNP K promoter fold into pH/K⁺-responsive tetraplexes: G-quadruplexes repress, i-motifs activate. hnRNP K binds its own i-motif sites with Sp1, suggesting autoregulation. Ligands flip the switch. #JBSD www.tandfonline.com/doi/full/10....

Wake Physics PhD student Banasree Mou presented her research in a poster, "Dynamical Effective Hamiltonian for Second Harmonic Generation in Quantum Magnets" at the Highly Frustrated Magnetism 2025 conference in Toronto, Canada!

The Next Gen Conversations: Albany @ Tech The Next Generation Conversations: Albany @ Louisiana Tech Professor Ramaswamy H. Sarma selected Louisiana Tech University to host the Next Generation Conversations thanks to the University’s location...

Join us for conversation & crawfish at
The 2nd Next Gen. Conversation in
Biomolecular Structure & Dynamics
Louisiana Tech University June 9-13, 2026! These continue Professor Sarma's hugely impactful Albany Conversations.
Remo Rohs will be the 2026 keynote speaker coes.latech.edu/albany-conve...

Non-Covalent Interactions and Helical Packing in Thiophene-Phenylene Copolymers: Tuning Solid-State Ordering and Charge Transport for Organic Field-Effect Transistors In this study, we introduce two thiophene-phenylene-thiophene (TPT) polymers designed to leverage noncovalent intramolecular interactions to regulate main-chain conformation and enhance solid-state ordering. By incorporating unsubstituted thiophene (T) or bithiophene (2T) units, we reveal striking divergence in the thermal, morphological, and optoelectronic properties of the resulting films, facilitated by these noncovalent interactions. Using a combination of computational and experimental approaches, we show that annealing yields remarkably different polymer conformations and, consequently, charge transport properties. TPT-T undergoes a significant structural transformation, adopting a more planar backbone conformation and a highly crystalline, edge-on molecular orientation. In contrast, the introduction of a single additional thiophene unit in TPT-2T leads to a more isotropic molecular orientation with a slight preference for face-on alignment, resulting in a heterogeneous film structure that hinders charge transport despite achieving tighter molecular packing. Remarkably, despite being composed of achiral components, TPT-2T develops chirality upon annealing, indicating the formation of a helical conformation. Organic field-effect transistor measurements reveal that the well-ordered alignment in annealed TPT-T films results in higher charge carrier mobility and a narrower distribution of mobility values than in TPT-2T. These findings provide critical insights into the structure–property relationships of conjugated polymers, offering guidance for optimizing molecular design and processing strategies for high-performance organic electronic materials.

Congrats to one of our Wake Physics PhD students, Mani Manikanta, for his first-author paper in Chemistry of Materials pubs.acs.org/doi/full/10.... !

Molecular modeling and simulation studies of SELEX-derived high-affinity DNA aptamers to the Ebola virus nucleoprotein Ebola viral disease (EVD) is a highly infectious and potentially fatal illness with a case fatality rate ranging from 25% to 90%. To effectively control its spread, there is a need for rapid, relia...

In Vol 43, Issue 9, In silico MD shows SELEX DNA aptamers bind Ebola NP: Apt1 KD 25 nM > Apt2 56 nM > Apt3 140 nM. Computation mirrors MST, speeding point-of-care EVD tests and showcasing in-silico/in-vitro synergy. #JBSD #MDSimulations www.tandfonline.com/doi/full/10....

Investigation of the interaction between S-isoalkyl derivatives of the thiosalicylic acid and human serum albumin S-isoalkyl derivatives of thiosalicylic acid (isopropyl-(L1), isobutyl-(L2) and isoamyl-(L3)) were selected in order to investigate the binding interaction with the human serum albumin (HSA) using ...

Spectroscopy and MD simulations reveal that S-isoalkyl thiosalicylic acid derivatives (L1–L3) bind HSA at Site I via static quenching. L3 shows the strongest, most stable interaction at Sudlow I, inducing notable conformational changes. #JBSD
www.tandfonline.com/doi/full/10....

GSLAlign: community detection and local PPI network alignment High throughput protein–protein interaction (PPI) profiling and computational techniques have resulted in generating a large amount of PPI network data. The study of PPI networks helps in understan...

GSLAlign, a new local PPI network aligner, combines GraphSAGE-based community detection with sequence-similarity alignment. It outperforms previous methods in semantic similarity, connectivity, and coverage—enhancing cross-species PPI comparison. #JBSD www.tandfonline.com/doi/full/10....

Investigating the combined effect of copper, zinc, and iron ions on truncated and full-length Aβ peptides: insights from molecular dynamics simulation The truncated Aβ1 − 16 peptide containing the metal-binding domain is frequently used in in silico and experimental investigations because it is more soluble and thus more suitable for studies in s...

MD simulations show that Cu²⁺ binds strongly to His13/His14 in full-length and truncated Aβ peptides. Zn²⁺ and Fe³⁺ modulate Cu²⁺ binding and reduce aggregation tendency, especially in Aβ₁₋₁₆. Truncation & metal ion synergy shape Aβ structure. #JBSD #MDSimulations www.tandfonline.com/doi/full/10....

MD simulations reveal that glucose-mediated glycation alters HSA structure—reducing α-helical content, distorting Sudlow sites, shifting Trp214 orientation, and disrupting domain mobility and hydration—potentially impairing ligand binding. #JBSD t.co/VJsY7rHWrg

Congrats ?

Could it be Introduction to Computational Chemistry by Frank Jensen ?

Could you be thinking of essentials of computational chemistry by Cramer ? I’m out of office so I can’t double-check my copy but I think it has those practical exercises.

Congrats to our PhD student Katherine Koch, who has been awarded a 2025 SPIE Woman in Optics Scholarship! @SPIEtweets @ajaykandada.bsky.social #physics #optics spie.org/membership/s...

QM/MM analysis reveals how LysRS discriminates between lysine and toxic ornithine: substrate-assisted self-cyclization edits Orn-AMP with a lower barrier (101.2 kJ/mol) vs. Lys-AMP (140.2 kJ/mol), enabling efficient pre-transfer proofreading. #JBSD #QMMM t.co/VgtW2aANZn

Comprehending conformational changes in EmrE, multidrug transporter at different pH: insights from molecular dynamics simulations EmrE is a small multidrug resistance (SMR) pump of antiparallel topology that confers resistance to a broad range of polyaromatic cations in Escherichia coli. Atomic-level understanding of conforma...

From Vol 43, Issue 8 MD simulations show that MGMT mutations alter structure and binding: L84F/K125E mimics wild-type in free form, but L84F alone shows distinct interactions with PCNA/DNA and the highest binding free energy—highlighting SNP-driven conformational shifts. #JBSD #MDSimulations

We are pleased at JBSD that Professor Dmitry O. Zharkov (Institute of Chemical Biology & Fundamental Medicine, SB RAS / Novosibirsk State University), a leading authority on DNA repair & DNA glycosylases, is continuing with us as an Editorial Board member. #JBSD #DNARepair #BaseExcisionRepair

We are pleased to welcome Professor Lynn Zechiedrich (Baylor College of Medicine), a leading expert in DNA topology, supercoiling & topoisomerases, to our JBSD Editorial Board. #JBSD #DNATopology #Topoisomerase #NucleicAcids www.bcm.edu/people-searc...