iiinova — where your digital self keeps evolving

Fred @salsbblue.bsky.social · 12/10/2026

HVLGAN reached 0.96 novelty, uniqueness and validity in the MOSES comparison at 90% training. Hole et al. #JBSD www.tandfonline.com/doi/full/10.... Audio: open.spotify.com/episode/1u5v...

Dark charcoal and gold JBSD infographic showing a labeled HVLGAN model schematic. Graph-based pocket embedding feeds SMILES representations into a model containing a latent GAN, H2S attention and a latent VAE, then produces abstract molecular-output tokens. In the MOSES benchmark at 90% training, Table 3 reports 0.96 novelty, 0.96 uniqueness and 0.96 validity. Teal highlights model layers and uniqueness. Source: Hole et al., Figures 2, 4 and 5, and Table 3.

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Fred @salsbblue.bsky.social · 08/10/2026

We’re hiring at Wake Forest Physics: tenure-track Assistant Professor in biophysics and/or materials science. Starts July 1, 2027. Apply by Nov. 15, 2026 for full consideration; review continues until filled. Full ad: apply.interfolio.com/194988

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Fred @salsbblue.bsky.social · 07/10/2026

TSR geometric keys improved neurotransmitter clustering across five datasets, each with seven classes and 20 structures per class. Reaux et al. #JBSD www.tandfonline.com/doi/full/10.... Audio: open.spotify.com/episode/0zdO...

Dark charcoal and gold JBSD infographic with a labeled TSR method schematic. Three abstract points form a triangle, leading to layered geometric keys and a branching shape-comparison tree. Five benchmark datasets each contain seven classes and 20 structures per class. TSR outperforms RMSD, USR and ROSHAMBO and is slightly ahead of Phase in this comparison. Teal distinguishes schematic elements. Source: Reaux et al., Methods, Section 3.6 and Figure 10.

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Fred @salsbblue.bsky.social · 06/10/2026

Gabriel Landi of the University of Rochester visited Wake Forest Physics on October 1, 2026, for “Quantum trajectories and stochastic thermal machines.” His talk connected quantum thermodynamics, measurement and feedback control. Photos from Olin 101.

A speaker stands beneath a projected title slide reading “Quantum trajectories and feedback control of stochastic thermal machines,” with Gabriel T. Landi and the University of Rochester listed below.

A speaker gestures toward a projected diagram of a quantum refrigerator and a target qubit. Visible slide questions ask how long cooling takes and the probability that it works. The top of the slide is outside the photograph.

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Fred @salsbblue.bsky.social · 05/10/2026

6e inhibited E. coli; 6h inhibited P. aeruginosa. Each reported MIC: 50 ± 2.5 µg/mL (mean ± SD). Makwana et al. #JBSD www.tandfonline.com/doi/full/10.... Audio: open.spotify.com/episode/6vZY...

Dark charcoal and gold JBSD infographic with a labeled assay schematic: pyrrolopyrimidine derivatives flow into a broth microdilution plate and two bacterial assay callouts. Compound 6e inhibits E. coli and compound 6h inhibits P. aeruginosa, each at a reported MIC of 50 ± 2.5 µg/mL (mean ± SD). Chloramphenicol has a mean MIC of 50 µg/mL in both strains. The study tested 14 derivatives. Bacteria and plate are conceptual illustrations. Source: Makwana et al., Table 1.

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Fred @salsbblue.bsky.social · 04/10/2026

Pablo Ruales and Isabelle Coughlin represented Wake Forest Physics at NCAM 2026, presenting work on black-hole polarization and thick accretion disks. Congratulations to both! physics.wfu.edu/2026/10/wake...

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Fred @salsbblue.bsky.social · 02/10/2026

Neohesperidin, quercetin and myricetin led both MMGBSA and umbrella-sampling rankings at dengue MTase. K. L. Joseph Libin et al. #JBSD www.tandfonline.com/doi/full/10.... Audio: open.spotify.com/episode/0u8e...

Dark charcoal and gold JBSD infographic. A labeled workflow schematic splits eight papaya-associated flavonoids into bound-state MMGBSA analysis and unbinding analysis using steered molecular dynamics and umbrella sampling. Both routes lead to the same top three: neohesperidin, quercetin and myricetin, in that order. The study targets dengue-virus NS5 methyltransferase. Source: K. L. Joseph Libin and colleagues, Tables 2 and 3.

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Fred @salsbblue.bsky.social · 30/09/2026

UM-4E led mean docking scores at four S. aureus targets. Hla: −9.70 kcal/mol versus −7.54 for UM-C162. Al Quwatli et al. www.tandfonline.com/doi/full/10.... Audio: open.spotify.com/episode/2ouQ...

Dark charcoal and gold JBSD infographic. A labeled screening schematic connects UM-4E in gold and UM-C162 in teal to Hla, SrtA, AgrA and SspA. UM-4E leads the mean docking scores across these four Staphylococcus aureus targets. Hla mean docking binding energies are −9.70 for UM-4E, −7.54 for UM-C162, −5.94 for curcumin and −5.17 for ACA, all in kcal/mol. The study used 100 docking runs per ligand–target pair. Source: Al Quwatli and colleagues, Figure 7.

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Fred @salsbblue.bsky.social · 28/09/2026

My colleague Wenjun Zhao speaks at Wake Forest Physics on Oct. 8 about geometry and heterogeneity in biological imaging. 4 p.m., Olin 101; reception 3:30 p.m., Olin Lobby. physics.wfu.edu/2026/09/octo...

Wake Forest Physics Colloquium flyer with a portrait of Prof. Wenjun Zhao, Department of Mathematics, Wake Forest University. “Some data-driven methods for quantifying geometry and heterogeneity in biological imaging.” Thursday, October 8, 2026, at 4 p.m. in Olin 101; reception at 3:30 p.m. in the Olin Lobby.

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Fred @salsbblue.bsky.social · 28/09/2026

kerC mean radius of gyration: ≈2.06 nm in [AMIM]Cl, ≈2.09 nm in water and ≈2.49 nm in [BMIM]Br (100–200 ns). Article: www.tandfonline.com/doi/full/10.... Audio: open.spotify.com/episode/7b0F... #JBSD

Dark-and-gold JBSD infographic with a labeled study schematic linking keratinase kerC to three solvent conditions. Mean radius of gyration over 100–200 ns was approximately 2.06 nm in [AMIM]Cl, close to 2.09 nm in water, and 2.49 nm in [BMIM]Br. Ionic liquids were at 0.5 M in 200 ns simulations. Gold, white and teal distinguish the conditions. Rai and Hasija, Volume 44, Issue 12; Section 3.2.5.1 and Figure 12.

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Fred @salsbblue.bsky.social · 23/09/2026

Bitopertin scored 1.382 for DAT and 0.794 for GlyT1 by Exponential Consensus Ranking across three docking programs. Article: www.tandfonline.com/doi/full/10.... Audio: open.spotify.com/episode/323O... #JBSD

Black-and-gold JBSD infographic with a labeled ranking schematic. A geometric Bitopertin node branches to DAT, ECR 1.382, in gold and GlyT1, ECR 0.794, in teal. Bitopertin scores higher for DAT than GlyT1. Two smaller annotations identify NFPS_2 as first for GlyT1 at ECR 1.896 and Org 24598_2 as first for GlyT2 at ECR 1.075. ECR combines ranks from AutoDock Vina, GOLD and DockThor. Source: Nascimento and colleagues, Section 3.3 and Figure 4.

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Fred @salsbblue.bsky.social · 21/09/2026

HEXA with pyrimethamine: average intermolecular H-bond counts were ≈3.8 for W474C, ≈1.8 for native and ≈2.2 for W485R in 500 ns simulations. Article: www.tandfonline.com/doi/full/10.... Audio: open.spotify.com/episode/0wwl... #JBSD

Black-and-gold JBSD infographic with a labeled study-workflow schematic. A screen of 158 missense variants leads to W474C and W485R. Both variants and a separate native HEXA reference enter 500 ns molecular dynamics analysis with pyrimethamine. Reported average backbone RMSD values are approximately 0.230 nm for native, 0.224 nm for W474C and 0.264 nm for W485R. Average intermolecular hydrogen-bond counts are approximately 1.8, 3.8 and 2.2, respectively. Gold highlights show W485R has the highest average backbone RMSD and W474C the highest average hydrogen-bond count. Source: S. Ranjani et al., Table 12.

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Fred @salsbblue.bsky.social · 18/09/2026

From a 9,390-compound Gwt1 screen, tivozanib reached MIC90 of 1 ± 0.5, 2 ± 1, and 1 ± 0.5 µg/mL against C. neoformans, C. albicans, and A. fumigatus. www.tandfonline.com/doi/full/10.... Audio: open.spotify.com/episode/59sY... #JBSD

Square JBSD infographic showing a conceptual Gwt1 pocket workflow that screens 9,390 compounds and identifies tivozanib and rosiglitazone. Their docking scores are −9.10 and −8.13 kcal/mol. A three-species MIC90 table lists tivozanib at 1 ± 0.5, 2 ± 1, and 1 ± 0.5 µg/mL, and rosiglitazone at 4 ± 1.5, 4 ± 2, and 1 ± 0.5 µg/mL, against C. neoformans, C. albicans, and A. fumigatus.

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Fred @salsbblue.bsky.social · 16/09/2026

Applications are open for Fall 2027 graduate study with Wake Forest Physics! Physics Ph.D. and M.S., plus the M.S. and graduate certificate in Quantum Information Sciences. Apply by Jan. 8, 2027: physics.wfu.edu/graduate-pro... physics.wfu.edu/graduate-pro...

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Fred @salsbblue.bsky.social · 16/09/2026

Rhapontigenin ranked 5th by docking score but 1st by mean computed MM-PBSA binding free energy in an Aβ42 model. Mean ranks do not establish statistical separation. www.tandfonline.com/doi/full/10.... Audio: open.spotify.com/episode/4tmB... #JBSD

Square black-and-gold JBSD infographic comparing five stilbenoids in an Aβ42 protofibril model. Colored curves connect each compound's docking-score rank on the left to its mean MM-PBSA binding-free-energy rank on the right. Rhapontigenin's gold curve rises from fifth to first: docking score −6.6 kcal/mol; computed MM-PBSA binding free energy −16.732 ± 5.807 kcal/mol. Piceid moves from first to third; astringin stays second; piceatannol moves from third to fourth; resveratrol moves from fourth to fifth. Labels reproduce the reported values and variation. Curves connect identities, not energy magnitudes; these computed rankings do not establish statistical separation. Based on the article's Tables 2 and 3.

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Fred @salsbblue.bsky.social · 15/09/2026

On Sept. 10, Wake Forest Physics alumnus Dr. Taylor Ordines of Johns Hopkins APL returned to campus for a career and research Q&A. He spoke about his work at APL, his path after Wake Forest, and the choices that shaped his career. Thanks for coming back, Taylor!

Dr. Taylor Ordines sits at the front of a lecture hall answering a question beside a faculty moderator, with audience members in the foreground.

A wide view from the back of a lecture hall shows students and faculty facing Dr. Taylor Ordines and a faculty moderator at the front.

Dr. Taylor Ordines sits beneath a periodic table speaking to the audience while a faculty moderator stands at the right.

A wide side view shows students and faculty gathered in a lecture hall for the Q&A with Dr. Taylor Ordines.

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Fred @salsbblue.bsky.social · 15/09/2026

Thank you to Prof. Martin Seifrid of NC State for visiting Wake Forest Physics on Sept. 3. His colloquium explored self-driving labs, uncertainty-aware machine learning, and data-driven design of organic mixed ionic-electronic conductors. #WFUPhysics

Prof. Martin Seifrid speaks beside the title slide for “Establishing the Data-Driven Organic Materials Lab” at Wake Forest University on September 3, 2026.

Prof. Martin Seifrid speaks to students and faculty in Olin 101 during the Wake Forest Physics colloquium.

Students and faculty gather for the reception before Prof. Martin Seifrid’s Wake Forest Physics colloquium.

Wake Forest Physics students and faculty talk over refreshments at the September 3 colloquium reception.

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Fred @salsbblue.bsky.social · 15/09/2026

Prof. Salvatore Vitale (MIT): “Use and abuse of gravitational-wave datasets” Sept. 17 | Reception 3:30 p.m., Olin Lobby | Talk 4 p.m., Olin 101 What can GWTC-5 tell us about binary black hole populations? physics.wfu.edu/2026/09/use-...

Flyer for a Wake Forest Physics Colloquium with a portrait of Prof. Salvatore Vitale of MIT. “Use and abuse of gravitational-wave datasets” is Thursday, September 17, 2026, at 4 p.m. in Olin 101, following a 3:30 p.m. reception in the Olin Lobby.

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Fred @salsbblue.bsky.social · 14/09/2026

Congratulations to my WFU colleague Alejandro Cárdenas-Avendaño on a $384,000 NASA grant for black-hole inspiral research and student opportunities with Marshall Space Flight Center. physics.wfu.edu/2026/09/alej... Image: Gemini (AI-generated).

AI-generated illustration of a small compact object beside a supermassive black hole, surrounded by looping gold orbital paths against a star field. NASA and Wake Forest emblems appear at lower right. Conceptual illustration created with Gemini and supplied by Alejandro Cárdenas-Avendaño.

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Fred @salsbblue.bsky.social · 14/09/2026

CBDPF pairs LoRA-adapted ProtT5 with a CNN for candidate dephosphorylation-site prediction. Reported dbPTM S/T accuracy: 98.72% vs 97.98% for fully fine-tuned ProtT5 (Table 4). doi.org/10.1080/0739... open.spotify.com/episode/0QE9... #JBSD

Square black-and-gold JBSD infographic about CBDPF for protein dephosphorylation-site prediction. A labeled computational-model schematic connects sequence windows, ProtT5, LoRA, a CNN, and site prediction. Gold labels identify CBDPF and turquoise labels identify fully fine-tuned ProtT5. Reported accuracy is 98.72% versus 97.98% on dbPTM S/T sites (Table 4), and 99.12% versus 98.43% on PhosphoSitePlus Y sites (Table 5). The schematic is adapted from Figure 1; no molecular structure is shown. Results are computational benchmarks, with no experimental test of phosphate removal.

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Fred @salsbblue.bsky.social · 09/09/2026

TCB-Kla predicts human lysine lactylation from sequence. Test accuracy: 82.11% full model vs 79.77% without multi-scale CNN. Predictions need experimental follow-up. doi.org/10.1080/0739... open.spotify.com/episode/4pI8... #JBSD

Square black-and-gold JBSD infographic for TCB-Kla. A peptide window centered on lysine feeds a Transformer encoder, multi-scale CNN, bidirectional LSTM, and fully connected classifier. Table 6 independent-test accuracy is 82.11% for the full model and 79.77% without the multi-scale CNN; full-model ROC AUC is 0.8983. The schematic is adapted from Figure 1. Authors: Shengli Zhang and Bin Sheng, Xidian University. DOI: 10.1080/07391102.2026.2645110.

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Fred @salsbblue.bsky.social · 08/09/2026

At Wake Forest this Thursday: Dr. Taylor Ordines (Johns Hopkins APL) on “Geometry and dynamics of attainable sets of interacting decision makers.” Sept. 10, 2026 • 4 p.m., Olin 101 Reception: 3:30 p.m., Olin lobby #WFUPhysics

Updated Physics Colloquium flyer featuring Dr. Taylor Ordines of Johns Hopkins Applied Physics Laboratory and “Geometry and dynamics of attainable sets of interacting decision makers.” Thursday, September 10, 2026, 4 p.m., Olin 101, Wake Forest University. Reception at 3:30 p.m. in the Olin lobby. Includes his portrait, talk abstract, and revised biography: Allegheny College physics degree in 2015, Wake Forest MBA in 2020 and Ph.D. in 2022, and his roles at APL.

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Fred @salsbblue.bsky.social · 07/09/2026

Raloxifene–STAT3 dynamics varied with its surroundings in three 100 ns simulations. Cα-RMSD was mostly 0.20–0.30 nm alone and 0.10–0.25 nm with cisplatin; with metformin, the range was 0.20–0.45 nm. doi.org/10.1080/0739... #JBSD

Black-and-gold JBSD infographic comparing three 100 ns simulations of raloxifene–STAT3. A labeled conceptual silhouette represents the complex, with gold, red, and teal annotations for the complex alone, metformin, and cisplatin. Reported Cα-RMSD ranges are 0.20–0.30, 0.20–0.45, and 0.10–0.25 nm, respectively. The schematic is not a molecular structure; the ranges are not confidence intervals. Experimental validation remains needed.

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Fred @salsbblue.bsky.social · 04/09/2026

Wake Forest Physics students: our first 2026–27 career event is Wednesday, Sept. 9, at noon in the Olin Physical Laboratory foyer. Taylor Ordines, a Wake Forest Physics graduate now at Johns Hopkins APL, will talk about career paths and work at APL. Free pizza.

Wake Forest Physics career event graphic for Dr. Taylor Ordines of the Johns Hopkins Applied Physics Laboratory. The event is Wednesday, September 9, 2026, at noon in the Physics foyer and is open to undergraduate and graduate students. Free pizza will be provided.

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Fred @salsbblue.bsky.social · 04/09/2026

Conus amadis venom had six PTM variants of α-conotoxin Am2005. In an Ac-AChBP model, MM-GBSA shifted from −89.9 to −194.2 kcal/mol in the top variant. The binding result is computational. doi.org/10.1080/0739... open.spotify.com/episode/3aVD... #JBSD

Square JBSD infographic over a conceptual molecular illustration. A gold α-conotoxin sits in a translucent receptor pocket, with colored points marking site-specific PTMs. Text compares modeled MM-GBSA binding estimates for Am2005 (−89.9 kcal/mol) and [P2O,P15O,E16γ]Am2161 (−194.2 kcal/mol), notes AggScore values of 12.5–49.7 across modeled variants, and states that six variants were detected by LC-ESI-MS/MS while structure and binding results were computational using Ac-AChBP as a nAChR proxy.

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Fred @salsbblue.bsky.social · 02/09/2026

At 2% EmimOAc, acetate clustered near the TtL active site (5.45 Å; g(r)=16.00). At 10%, TtL–acetate H-bonds reached 49.44 ± 7.81, supporting a shift from competitive to noncompetitive inhibition. www.tandfonline.com/doi/full/10.... #JBSD

Square JBSD results card asking how EmimOAc concentration shifts acetate binding around Thermus thermophilus laccase, with PDB 2XU9 named as the starting model. The study compares three 500 ns systems: water, 2% EmimOAc, and 10% EmimOAc. At 2%, acetate reached the active site at an RDF peak distance of 5.45 Å with g(r)=16.00; earlier experiments reported 50% activity retained, and the authors interpret the simulation as competitive inhibition. At 10%, TtL–acetate hydrogen bonds were 49.44 ± 7.81 versus 15.87 ± 5.11 at 2%; earlier experiments reported 10% activity retained, and the authors interpret the simulation as surface-associated noncompetitive inhibition. The card notes that predicted mutation targets require experimental validation.

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Fred @salsbblue.bsky.social · 31/08/2026

In a 600 ns simulation, the DNA–topoisomerase IB complex stabilized after 150 ns. MM/GBSA gave a binding free energy of −43.96 ± 1.56 kcal/mol. The proposed rotation mechanism remains computational. Article: doi.org/10.1080/0739... #JBSD

Square JBSD results card about a 600 ns computational study of DNA rotation by human topoisomerase IB using the PDB 1A36 model. Three panels report that the DNA and enzyme stabilized after 150 ns, with mean deviations up to 3.5 Å and 2.4 Å; the MM/GBSA binding free-energy estimate was −43.96 ± 1.56 kcal/mol; and Lys318 contributed −14.2 kcal/mol in the per-residue decomposition. The card labels controlled rotation as the authors’ interpretation and notes that experimental validation is still needed.

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Fred @salsbblue.bsky.social · 31/08/2026

Saturday's Physics Graduate Student Symposium brought talks and posters together at Farrell Hall. Our graduate students discussed work on black holes, spectroscopy, climate, protein folding, organic materials, quantum magnets, and more.

Photo from the 2026 Wake Forest Physics Graduate Student Symposium at Farrell Hall.

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Fred @salsbblue.bsky.social · 31/08/2026

Our Fall 2026 Welcome Colloquium began with four student research talks, including presentations on spin qubits and black-hole modeling and imaging. We also welcomed seven new physics graduate students. #WakeForest #Physics

Wide view of Olin 101 as a student presents research on noise in spin qubits to faculty, staff, and students.

A department staff member speaks to the seminar about building access and the machine shop course.

A student presenter stands beneath a “Black Hole Imaging” slide in Olin 101.

Small groups talk in the Olin Physical Laboratory lobby before or after the Welcome Colloquium.

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Fred @salsbblue.bsky.social · 28/08/2026

My FYS 100 students started with “What is a supercomputer?” and ended up among the racks and network connections inside Wake Forest's data center. Thanks to the IS/HPC team for showing us the hardware behind computational research. #HPC #Physics #WakeForest

A Wake Forest HPC staff member speaks at a laptop beside a projected slide during the opening presentation.

Wide classroom view of FYS 100 students seated at tables while two presenters introduce high-performance computing on a projected slide.

A Wake Forest HPC staff member points toward a server rack.

Students gather in a data-center aisle around an HPC staff member.

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Fred @salsbblue.bsky.social · 28/08/2026

AI can make disorder look folded. For α-synuclein, mean Rg was 23.3/19.9 Å with AlphaFlow/AlphaFlow-MD vs 34.2/35.9 Å with AFflecto/Ensemblify—closer to ~33 Å experimentally. None captured every ensemble feature. doi.org/10.1080/0739... #JBSD

Square JBSD scientific results card comparing four AI pipelines for 140-residue α-synuclein. A four-column comparison reports mean radius of gyration: AlphaFlow 23.3 ± 4.3 Å, AlphaFlow-MD 19.9 ± 2.1 Å, AFflecto 34.2 ± 8.0 Å, and Ensemblify 35.9 ± 7.7 Å, with an experimental comparison near 33 Å. AFflecto and Ensemblify are shown as expanded, coil-rich ensembles with broader shape-space coverage. A note states that no pipeline captured every intramolecular contact or experimental secondary-structure value. Any protein-chain icons are labeled schematic ensembles.

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Fred @salsbblue.bsky.social · 26/08/2026

Wake Forest Physics graduate students present their work this Saturday, Aug. 29, at Farrell Hall. Talks and posters cover black holes, spectroscopy, climate, protein folding, organic materials, quantum magnets, and more. Program: sites.google.com/wfu.edu/phyg...

Cover of the 2026 Wake Forest Physics Graduate Student Symposium program, Saturday, August 29, 2026, in Farrell Hall.

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Fred @salsbblue.bsky.social · 26/08/2026

An MD preprocessing step inverted a strong/weak ranking: R² 0.113 vs 0.553. RBT preserved the expected order, 1.00 vs 0.908. A 50 ns protein–ligand case study then separated positional from dipole motion. www.tandfonline.com/doi/full/10.... #JBSD

Square JBSD infographic titled “RBT Preserves Spatial Motion Correlation.” Top panels use aligned and scattered trajectory arrows to compare the designed RSW model: RBT gives average R² values of 1.00 for strong and 0.908 for weak positional motion, while RMSD-based preprocessing gives the misleading reversal 0.113 and 0.553. Bottom panels show the real 50 ns Q108R CRBP1–atREA case study: Lys-40 positional average R² is 0.903 and Arg-108 dipole-direction average R² is 0.763. A footer notes that the method is post hoc and has limited applicability to unfolding, intrinsically disordered proteins, and other large topological changes. The trajectory arrows are schematic; no molecular structure is shown.

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Fred @salsbblue.bsky.social · 24/08/2026

Cooling strengthened alanine hydration. At 283.15 K, relative association rose 0.9806→0.9951 from 0.15→0.30 C(M), then varied nonmonotonically at higher concentrations. www.tandfonline.com/doi/full/10.... #JBSD #Biophysics

Square JBSD results card titled “How do temperature and concentration reorganize alanine–water hydration?” A measurement strip reports 5-MHz pulse-echo ultrasonics, 278.15–303.15 K, and 0.15–0.75 C(M). Three findings state: at 283.15 K, relative association rises from 0.9806 at 0.15 C(M) to 0.9951 at 0.30 C(M) and then varies nonmonotonically at 0.45–0.75 C(M); activation free energy is 2.07–2.12 kcal mol−1 and activation enthalpy is 0.48–0.57 kcal mol−1; lower temperatures support more structured hydration, while hydration number decreases as temperature and concentration increase. A limitation notes that the Pasynski calculation assumes zero compressibility for hydration-shell water. No molecular structure is depicted.

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Fred @salsbblue.bsky.social · 21/08/2026

Varespladib neutralized snake-venom PLA2 100% at 1:10, but not bee PLA2 at tested doses. Tyr87/Ile91 redirect its conserved Ca2+-centered pose in bee PLA2. Paper: doi.org/10.1080/0739... Audio: open.spotify.com/episode/2Tgc... #JBSD

Square JBSD infographic titled “Why does varespladib inhibit snake—but not bee—venom PLA2?” A two-column schematic contrasts a conserved calcium-centered varespladib pose in snake-venom PLA2, involving His47, Asp48, Gly29, and Gly31, with an alternative bee-venom PLA2 pose caused by steric clash at Tyr87 and Ile91. Three findings report a conserved pose across nine snake PLA2 structures; 100% snake-venom PLA2 neutralization at a 1:10 ratio with no bee catalytic neutralization at tested doses; and 72–80% inhibition of snake-venom-induced reactive oxygen species plus 26–30% inhibition of membrane depolarization in C. elegans. The molecular view is schematic.

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Fred @salsbblue.bsky.social · 19/08/2026

How does acidity redirect transthyretin aggregation? T4 binding fell from 50.0 ± 0.6% at pH 7.4 to 28.2 ± 0.8% at pH 4.4, then disappeared at ≤3.3. pH 4.4 favored amorphous clusters; pH 3.3 favored ThT-positive fibrils. Listen: open.spotify.com/episode/0Ybl...

Scientific infographic showing how acidic pH destabilizes transthyretin: stable from pH 8.0 to 6.6, dense amorphous clusters at pH 4.4, fibril-rich ThT-positive networks at pH 3.3, and extensive denaturation at pH 2.2.

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Fred @salsbblue.bsky.social · 18/08/2026

Call for papers: JBSD’s new Article Collection seeks mechanistic studies linking disease-associated variants to biomolecular structure, dynamics, allostery, function and molecular rescue. Submit and select the collection: rp.tandfonline.com/submission/c...

Four-stage schematic showing a disease-associated variant perturbing biomolecular structure and dynamics, disrupting allosteric communication and function, followed by a targeted molecular intervention that restores native-like dynamics and function.

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Fred @salsbblue.bsky.social · 17/08/2026

Longer heparin chains strengthened simulated SARS-CoV-2 RBD binding in DNA-origami nanocomplexes: ΔGbind shifted from −36.9 to −170.9 kJ/mol and rupture force from ~350 to ~750 pN. 🎧 open.spotify.com/episode/4ID8... #JBSD

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Fred @salsbblue.bsky.social · 14/08/2026

Six 200-ns simulations show how Aβ25–35 β-barrels disrupt POPC/POPG membranes: shallow barrels detach within 8–10 ns, deeper barrels remain embedded, and local effects reach ~1 nm while global thickness stays stable. 🎧 open.spotify.com/episode/6XZT... #MolecularDynamics

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Fred @salsbblue.bsky.social · 12/08/2026

Three 500-ns simulations show cGAS-DNA monomers rotate DNA ~40° and remain inactive, while long DNA raises the disassembly barrier from ~131 to 174 kcal/mol. New JBSD Audio Overview: open.spotify.com/episode/37RE...

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Fred @salsbblue.bsky.social · 10/08/2026

Heated coarse-grained MD + deep mutational scanning produced the HY29_M3 antibody variant for stronger CXCR2 binding. A43P/L47V/F98W shift MM-GBSA from −36.02 to −94.09 kcal/mol. Listen: open.spotify.com/episode/1uY0...

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Fred @salsbblue.bsky.social · 07/08/2026

Using protein dynamics in RFdiffusion raised stable KRAS binder designs from 30% to 60%. Even the lowest-ranked dynamic design had a 42% larger buried interface and 57% more H-bonds than the best static design. New JBSD Audio Overview: open.spotify.com/episode/1JTM...

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Fred @salsbblue.bsky.social · 05/08/2026

How can glycation weaken ApoE3’s lipid and heparin binding? In 1-µs simulations, MGH1 modifications opened the NT–CT interface; AP217 reached a 42.8 Å energy-minimum gap versus 13.3 Å native. New JBSD Audio Overview: open.spotify.com/episode/11Ns...

Scientific infographic titled How MGH1 Glycation Reshapes ApoE3, comparing the HelixC1-lock distance, final energy-minimum domain-gap distances for native and glycated ApoE3 systems, and structural changes affecting lipid and heparin binding.

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Fred @salsbblue.bsky.social · 03/08/2026

How do temperature and water-model polarity shape liposome self-assembly? Javadi, Ramezani & Darvishi report 800 ns at 300 K vs 250 ns at 400 K, with spherical vs ellipsoidal vesicles across Martini water models. 🎧 open.spotify.com/episode/1lm1... #JBSD

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Fred @salsbblue.bsky.social · 31/07/2026

TMAO made recombinant urate oxidase more compact and increased Vmax (1.61→2.39) and kcat (5.36→7.97), while Km rose and kcat/Km fell (95.51→75.24). Explore the integrated experiments, 100-ns MD, and docking in the new JBSD Audio Overview: open.spotify.com/episode/4Dfp...

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Fred @salsbblue.bsky.social · 30/07/2026

And with our celebration of Dr. Lynch, Summer 2026 defenses are a wrap! Congrats to Drs. Cai, Chapman, Ganter, Lynch, and Siggia!

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Fred @salsbblue.bsky.social · 29/07/2026

Cory Lynch, Dr. Natalie Holzwarth's final student, is defending! That's our fifth and final PhD defense for the summer. More to come in the Fall and Spring!

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Fred @salsbblue.bsky.social · 29/07/2026

How might KISS1 coordinate transcription factors in triple-negative breast cancer? Shah et al. combine HADDOCK docking, 150-ns MD, and MDA-MB-231 expression assays. CDX2 scored −144.2 with a 2526.5 Å² interface. Listen: open.spotify.com/episode/727J...

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Fred @salsbblue.bsky.social · 28/07/2026

Owen from Steve Winter's group is defending!

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Fred @salsbblue.bsky.social · 27/07/2026

Congrats to Dr. Siggia!

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