Publications

Refereed Papers & Preprints	Book Chapters & Proceedings

Refereed Papers & Preprints
2021

Amyloid-β peptide dimers undergo a random coil to β-sheet transition in the aqueous phase but not at the neuronal membrane
H. Fatafta, M. Khaled, M. C. Owen, A. Sayyed-Ahmad, B. Strodel
Proc. Nat. Acad. Sci. USA 118, e2106210118 (2021) [link]

Energy landscapes of protein aggregation and conformation switching in intrinsically disordered proteins
B. Strodel
J. Mol. Biol. 433, 167182 (2021) [link]

Disorder-to-order transition of the amyloid-β peptide upon lipid binding
H. Fatafta, B. Kav, B.F. Bundschuh, J. Loschwitz, B. Strodel
Biophys. Chem., accepted (2021)

The influences of sulphation, salt type, and salt concentration on the structural heterogeneity of glycosaminoglycans
S. Samantray, O. O. Olubiyi, B. Strodel
Int. J. Mol. Sci., accepted (2021)

Amyloid-type Protein Aggregation and Prion-like Properties of Amyloids
D. Willbold, B. Strodel, G. F. Schröder, W. Hoyer, H. Heise
Chem. Rev. 121, 13, 8285-8307 (2021 [link]

The Effects of Different Glycosaminoglycans on the Structure and Aggregation of the Amyloid-β (16-22) Peptide
S. Samantray, B. Strodel
J. Phys. Chem. B 125, 21, 5511-5525 (2021) [link]

Dataset of AMBER force field parameters of drugs, natural products and steroids for simulations using GROMACS
J. Loschwitz, A. Jäckering, M. Keutmann, M. Olagunju, O. O. Olubiyi, B Strodel
Data in Brief 35, 106948 (2021) [link]

Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis
P. H. Nguyen, A. Ramamoorthy, B. R. Sahoo, J. Zheng, P. Faller, J. E. Straub, L. Dominguez, J.-E. Shea, N. V. Dokholyan, A. De Simone, B. Ma, R. Nussinov, S. Najafi, S. Tung Ngo, A. Loquet, M. Chiricotto, P. Ganguly, J. McCarty, M. Suan Li, C. Hall, Y. Wang, Y. Miller, S. Melchionna, B. Habenstein, S. Timr, J. Chen, B. Hnath, B. Strodel, R. Kayed, S. Lesné, G. Wei, F. Sterpone, A. J. Doig, P. Derreumaux
Chem. Rev. 121, 2545-2647 (2021) [link]

Novel Inhibitors of the Main Protease of SARS-CoV-2 Identified via a Molecular Dynamics Simulation-Guided in Vitro Assay
J. Loschwitz, A. Jäckering, M. Keutmann, M. Olagunju, R. J. Eberle, M. A. Coronado, O. O. Olubiyi, B. Strodel
Bioorg. Chem. 111, 104862 (2021) [link]

Thermodynamics and kinetics of the amyloid-β peptide revealed by Markov state models based on MD data in agreement with experiment
A. Paul, S. Samantray, M. Anteghini, B. Strodel
Chem. Sci. 12, 6652-6669 (2021) [link]

Molecular dynamics studies for enhancing the anticancer drug efficacy: Toward designing a new carbon nanotube-based paclitaxel delivery system
L. Tohidifar, B. Strodel
J. Mol. Liquids, 323, 114638 (2020) [link]

Amyloid aggregation simulations: challenges, advances and perspectives
B. Strodel
Curr. Opin. Struct. Biol., 67:145-152 (2021) [link]

2020

Performance of Markov State Models and Transition Networks on Characterizing Amyloid Aggregation Pathways from MD Data
A.-M. Illig, B. Strodel
J. Chem. Theory Comput. 16, 7825-7839 (2020) [link]

Different force fields give rise to different amyloid aggregation pathways in molecular dynamics simulations
S. Samantray, F. Yin, B. Kav, B. Strodel
J. Chem. Inf. Model. 60, 6462-6475 (2020) [link]

β-Turn mimetic synthetic peptides as amyloid-β aggregation inhibitor/strong>i
S. Deike, S. Rothemund, B. Voigt, S. Samantray, B. Strodel, W.H. Binder
Bioorganic Chemistry 101, 104012 (2020) [link]

Molecular dynamics simulations of protein aggregation: protocols for simulation setup and analysis with Markov state models and transition networks
S. Samantray, W. Schumann, A.-M. Illig, M. Carballo-Pacheco, A. Paul, B. Barz, B. Strodel
bioRxiv, DOI:10.1101/2020.04.25.060269 (2020) [link]

High Throughput Virtual Screening to Discover Inhibitors of the Main Protease of the Coronavirus SARS-CoV-2
O. O. Olubiyi, M. Olagunju, M. Keutmann, J. Loschwitz, B. Strodel
Molecules 25, 3193 (2020) [link]

Symmetry-breaking transitions in the early steps of protein self-assembly
C. La Rosa, M. Condorelli, G. Compagnini, F. Lolicato, D. Milardi, T. Nhu Do, M. Karttunen, M. Pannuzzo, A. Ramamoorthy, F. Fraternali, F. Collu, H. Rezaei, B. Strodel, A. Raudino
Eur. Biophys. J. 49, 175-191 (2020) [link]

Role of oxidized Gly25, Gly29 and Gly33 residues on the interactions of Aβ-42 with lipid membranes
H. Fatafta, C. Poojari, A. Sayyed-Ahmad, B. Strodel, M.C. Owen
ACS Chem. Neurosci. 11, 535-548 (2020) [link]

2019

Rational Drug Design of Peptide-Based Therapies for Sickle Cell Disease
O.O. Olubiyi, M.O. Olagunju, B. Strodel
Molecules 24, 4551 (2020) [link]

Biochemical and structural characterization of murine GBP7, a guanylate binding protein with an elongated C-terminal tail
L. Legewie, J. Loschwitz, N. Steffens, M. Prescher, X. Wang, S.H.J. Smits, L. Schmitt, B. Strodel, D. Degrandi, K. Pfeffer
Biochem. J. 476, 3161-3182 (2019) [link]

Large-scale, dynamin-like motions of the human guanylate binding protein 1 revealed by multi-resolution simulations
B. Barz, J. Loschwitz, B. Strodel
PLOS Comp. Biol., 15, e1007193 (2019) [link]

Solution structure of the autophagy-related protein LC3C reveals a polyproline II motif on a mobile tether with phosphorylation site
C. Krichel, C. Möckel, O. Schillinger, P. F. Huesgen, H. Sticht, B. Strodel, O. H. Weiergräber, D. Willbold, P. Neudecker
Sci. Rep., 9, 1-15 (2019) [link]

Effects of in vivo conditions on amyloid aggregation
M.C. Owen, D. Gnutt, M. Gao, S.K.T.S. Wärmländer, J. Jarvet, A. Gäslund, R. Winter, S. Ebbinghaus, B. Strodel
Chem. Soc. Rev., 8, 3946-3996 (2019) [link]

Interference with Amyloid-β Nucleation by Transient Ligand Interactin
T. Zhang, J. Loschwitz, B. Strodel, L. Nagel-Steger, D. Willbold
Molecules, 24, 2129 (2019) [link]

Transition Metal Ion Interactions with Disordered Amyloid-β Peptides in the Pathogenesis of Alzheimer´s Disease: Insights from Computational Chemistry Studies
B. Strodel and O. Coskuner
J. Chem. Inf. Model., 59, 1782-1805 (2019) [link]

Automated Markov state models for molecular dynamics simulations of aggregation and self-assembly
U. Sengupta, M. Carballo-Pacheco, B. Strodel
J. Chem. Phys., 150, 115101 (2019) [link]

Interaction of carbohydrate-binding modules with poly(ethylene terephthalate)
J. Weber, D. Petrovic, B. Strodel, S.H.J. Smits, S. Kolkenbrock, C. Leggewie, K.-E. Jaeger
Appl. Microbiol. Biotechnol., accepted (2019)

Integrated NMR, Fluorescence, and Molecular Dynamics Benchmark Study of Protein Mechanics and Hydrodynamics
C. Möckel, J. Kubiak, O. Schillinger, R. Kühnemuth, D. Della Corte, G. F. Schröder, D. Willbold, B. Strodel, C. A. M. Seidel, P. Neudecker
J. Phys. Chem. B, 123: 1453-1480 (2010) [link]

Structural Studies of Autophagy-Related Proteins
M. Schwarten, O. H. Weiergräber, D. Petrovic, B. Strodel, D. Willbold
Autophagy. Methods Mol. Biol. 180: 17-56 (2019) [link]

2018

Loop Motion in Triosephosphate Isomerase is not a Simple Open and Shut Case
Q. Liao, Y. Kulkarni, U. Sengupta, D. Petrovic, A. J. Mulholland, M. W. van der Kamp, B. Strodel, and S. C. L. Kamerlin
J. Am. Chem. Soc., 140: 15889-15903 (2018) [link]

On the Applicability of Force Fields to Study the Aggregation of Amyloidogenic Peptides Using Molecular Dynamics Simulations
M. Carballo-Pacheco, A. E. Ismail, B. Strodel
J. Chem. Theory Comput., 14: 6063-6075 (2018) [link]

Amyloid-β Peptide Interactions with Amphiphilic Surfactants: Electrostatic and Hydrophobic Effect
N. Österlund, Y. S. Kulkarni, A. D. Misiaszek, C. Wallin, D. M. Krüger, Q. Liao, F. Mashayekhy Rad, Jüri Jarvet, B. Strodel, S. K. T. S. Wärmländer, L. L. Ilag, S. C. L. Kamerlin, A. Gräslund
ACS Chem. Neurosci., 9: 1680-1692 (2018) [link]

Schistosomiasis: Snail-vector control, molecular modelling and dynamic studies of bioactive N-acetylglycoside saponins from Tetrapleura tetraptera
B.J. Taiwo, O.O. Olubiyi, X. Wang, F.A. Fisusi, A. Ganiyu, F.R. Van Heerden, B. Strodel
Comput. Biol. Chem., 77: 363-372 (2018) [link]

Aβ under stress: the effects of acidosis, Cu²⁺-binding, and oxidation on amyloid β-peptide dimers
Q. Liao, M.C. Owen, S. Bali, B. Barz, B. Strodel
Chem. Commun., 54: 7766-7769 (2018) [link]

How accurately do force fields represent protein side chain ensembles?
D. Petrovic, X. Wang, B. Strodel
Proteins: Struct. Func. Bioinf., 86: 935-944 (2018) [link]

Physiologically-Relevant Levels of Sphingomyelin, but not GM1, Induce a β-Sheet-Rich Structure in the Amyloid-β(1-42) Monomer
M.C. Owen, W. Kulig, C. Poojari, T. Rog, B. Strodel
BBA - Biomembranes, 1860: 1709-1720 (2018) [link]

Structural insights from lipid-bilayer nanodiscs link α-Synuclein membrane binding modes to amyloid fibril formation
T. Viennet, M.M. Wördehof, B. Uluca, . Poojari, H. Shaykhalishahi, B. Strodel, H. Heise, A.K. Buell, W. Hoyer, M. Etzkorn
Communications Biology, 1: 44 (2018) [link]

Markov models for the elucidation of allosteric regulation
U. Sengupta, B. Strodel
Philos. Trans. Royal Soc., 373: 20170178 (2018) [link]

Simulation-guided design of cytochrome P450 for chemo- and regioselective macrocyclic oxidation
D. Petrovic, A. Bokel, M. Allan, V. B. Urlacher, B. Strodel
J. Chem. Inf. Model., 58: 848-858 (2018) [link]

Cholesterol Protects the Oxidized Lipid Bilayer From Water Injury: An All-Atom Molecular Dynamics Study
M.C. Owen, W. Kulig, T. Rog, I. Vattulainen, B. Strodel
J. Membr. Biol., 251: 521-534 (2018) [link]

DNP-Enhanced MAS NMR: A Tool to Snapshot Conformational Ensembles of a-Synuclein in Different States
B. Uluca, T. Viennet, D. Petrovic, H. Shaykhalishahi, F. Weirich, A. Gönülalan, B. Strodel, M. Etzkorn, W. Hoyer, H. Heise
Biophys. J., 114: 1614-1623 (2018) [link]

Pathways of Amyloid-β Aggregation Depend on Oligomer Shape
B. Barz, Q. Liao, B. Strodel
J. Am. Chem. Soc., 140: 319-327 (2018) [link]

2017

Learning From Simulations.
B. Strodel
Pan European Networks: Health, 02: 91-92 (2017) [PDF]

Extending the Nonbonded Cationic Dummy Model to Account for Ion-Induced Dipole Interactions
Q. Liao, A. Pabis, B. Strodel, S.C.L. Kamerlin
J. Phys. Chem. Lett., 8: 5408-5414 (2017) [link]

Molecular Dynamics Simulations Reveal Key Roles of the Interleukin-6 Alpha Receptor in the Assembly of the Human Interleukin-6 Receptor Complex
O. Schillinger, V. Panwalkar, B. Strodel, A. Dingley
J. Phys. Chem. B, 121: 8113-8122 (2017) [link]

Shuffling Active Site Sub-State Populations Impacts Catalytic Activity: The Case of Glucose Oxidase
D. Petrovic, D. Frank, S.C.L. Kamerlin, K. Hoffmann, & B. Strodel
ACS Catal., 7: 6188-6197 (2017) [link]

Enzyme Architecture: Modeling the Operation of a Hydrophobic Clamp in Catalysis by Triosephosphate Isomerase
Y. Kulkarni, Q. Liao, D. Petrovic, D.M. Krüger, B. Strodel, T.L. Amyes, J. Richard, S.C.L. Kamerlin
J. Am. Chem. Soc., 139: 10514-10525 (2017) [link]

Aβ42 pentamers/hexamers are the smallest detectable oligomers in solution
M. Wolff, B. Zhang-Haagen, C. Decker, B. Barz, M. Schneider, R. Biehl, A. Radulescu, B. Strodel, D. Willbold, & L. Nagel-Steger
Sci. Rep., 7: 2493 (2017) [link]

Protein Stability and Unfolding Following Glycine Radical Formation/strong>
M.C. Owen, I.G. Csizmadia, B. Viskolcz, & B. Strodel
Molecules, 22: 655 (2017) [link]

A combination of mutational and computational scanning guides the design of an artificial ligand-binding controlled lipase
M. Kaschner, O. Schillinger, T. Fettweiss, C. Nutschel, F. Krause, A. Fulton, B. Strodel, A. Stadler, K.-E. Jaeger, & U. Krauss
Sci. Rep., 7: 42592 (2017) [link]

Epigallocatechin-3-gallate preferentially induces aggregation of amyloidogenic immunoglobulin light chains
M. Hora, M. Carballo Pacheco, B. Weber, V. K. Morris, A. Wittkopf, J. Buchner, B. Strodel & B. Reif
Sci. Rep., 7: 41515 (2017) [link]

Conformational Transitions of the Amyloid-β Peptide Upon Copper(II) Binding and pH Changes.
Q. Liao, M. C. Owen, O. O. Olubiyi, B. Barz, & B. Strodel
Israel J. Chem., 57: 771-784 (2017) [link]

Comparison of force fields for Alzheimer's Aβ42 : a case study for intrinsically disordered proteins.
M. Carballo Pacheco & B. Strodel
Protein Sci., 26: 174-185 (2017) [link]

Investigating structure and dynamics of Atg8 family proteins.
O. H. Weiergräber, M. Schwarten, B. Strodel & D. Willbold
Methods Enzymol., 587: 115-142 (2017) [link]

2016

Topology and parameter data of thirteen non-natural amino acids for molecular simulations with CHARMM22
O. O. Olubiyi & B. Strodel
Data in Brief, 9, 642-647 (2016) [link]

A one-pot two-step hydroxylation of the macrocyclic diterpenoid β-cembrenediol catalyzed by P450 BM3 mutants
Le-Huu, D. Petrovic, B. Strodel & V. Urlacher
ChemCatChem, 8, 3755-3761 (2016) [link]

Radical Formation Initiates Solvent-Dependent Unfolding and β-Sheet Formation in a Model Helical Peptide
M. C. Owen, B. Strodel, I. G. Csizmadia & B. Viskolcz
J. Phys. Chem. B, 120, 4878-4889 (2016) [link]

Understanding Amyloid-β Oligomerization at the Molecular Level: the Role of the Fibril Surface.
B. Barz and B. Strodel
Chem Eur J, 22, 8768-8772 (2016) [link]

Characterization of Mn(II) ion Binding to the Amyloid-β Peptide in Alzheimer’s Disease
C. Wallin, Y.S. Kulkarni, A. Abelein, J. Jarvet, Q. Liao, B. Strodel, L. Olsson, J. Luo, J.P. Abrahams, S.B. Sholts, P.M. Roos, S.C.L. Kamerlin, A. Gräslund, S.K.T.S. Wärmländer
J Trace Elem Med Biol, 38: 183-193 (2016) [link]

Evaluation of the coarse-grained OPEP force field for protein-protein docking
P. Kynast, P. Derreumaux and B. Strodel
BMC Biophysics, 9:4 (2016) [link]

Advances in the Simulation of Protein Aggregation at the Atomistic Scale
M. Carballo-Pacheco and B. Strodel
J. Phys. Chem. B, 120, 2991–2999 (2016) [link]

An account of amyloid oligomers: facts and figures obtained from experiments and simulations
L. Nagel-Steger, M. C. Owen, and B. Strodel
ChemBioChem, 17, 657-676 (2016) [link]

Structural features determining thermal adaptation of esterases
F. Kovacic, A. Mandrysch, C. Poojari, B. Strodel, K.E. Jaeger
Protein Eng Des Sel., 29, 65-76 (2016) [link]

2015

Conformational Polymorphism in Autophagy-Related Protein GATE-16
P. Ma, O. Schillinger, M. Schwarten, J. Lecher, R. Hartmann, M. Stoldt, J. Mohrlüder, O. Olubiyi, B. Strodel, D. Willbold, and O. H. Weiergräber.
Biochemistry, 54, 5469–5479 (2015) [link]

Oligomer Formation of Toxic and Functional Amyloid Peptides Studied with Atomistic Simulations
M. Carballo-Pacheco, A. Ismail, and B. Strodel.
J. Phys. Chem. B, 119, 9696-9705 (2015) [link]

Development and Application of a Nonbonded Cu2+ Model That Includes the Jahn–Teller Effect
Q. Liao, S.C.L. Kamerlin, and B. Strodel.
J. Phys. Chem. Lett., 6, 2657–2662 (2015) [link]

Amyloid β Protein and Alzheimer’s Disease: When Computer Simulations Complement Experimental Studies
Nasica-Labouze J, Nguyen PH, Sterpone F, Berthoumieu O, Buchete NV, Coté S, De Simone A, Doig AJ, Faller P, Garcia A, Laio A, Mai SL, Melchionna S, Mousseau N, Mu Y, Paravastu A, Pasquali S, Rosenman DJ, Strodel B, Tarus B, Viles JH, Zhang T, Wang C, Derreumaux P.
Chem. Rev., 115, 3518-3563 (2015) [link]

2014

Extension of the FACTS implicit solvation model to membranes
M. Carballo Pacheco, I. Vancea, and B. Strodel.
J. Chem. Theory Comput., 10, 3163-3176 (2014) [link]

Protein structure prediction: assembly of secondary structure elements by basin-hopping
F. Hoffmann, I. Vancea, S.G. Kamat, and B. Strodel.
Chem. Phys. Chem., 15, 3378–3390 (2014) [link]

Early amyloid β-protein aggregation precedes conformational change
B. Barz, O. Olubiyi, and B. Strodel.
Chem. Commun., 50, 5373-5375 (2014) [link]
This communication is part of themed collection: 2014 Emerging Investigators.

A Kinetic Approach to the Sequence–Aggregation Relationship in Disease-related Protein Assembly
B. Barz, D.J. Wales, and B. Strodel.
J. Phys. Chem. B., 118, 1003-1011 (2014) [link]

Book Review: Protein-Protein Interactions in Drug Discovery.
B.Strodel.
ChemBioChem, 15, 472-473 (2014) [link]

Amyloid aggregation inhibitory mechanism of arginine-rich D-peptides
O. Olubiyi, D. Frenzel, D. Bartnik, J.M. Glück, O. Brener, L. Nagel-Steger, S.A. Funke, D. Willbold, and B. Strodel.
Curr. Med. Chem., 21, 1448-1457 (2014) [link]

2013

Interaction of Bcl-2 with the Autophagy-Related Protein GABARAP -- Biophysical Characterization and Functional Implications
Ma, P.; Schwarten, M.; Schneider, L.; Boeske, A.; Henke, N.; Lisak, D.; Weber, S.; Mohrluder, J.; Stoldt, M.; Strodel, B.; Methner, A.; Hoffmann, S.; Weiergraber, O. H.; Willbold, D.
J. Biol. Chem., 113, 1-26 (2013) [link]

Membrane permeation induced by aggregates of human islet amyloid polypeptides
C. Poojari, D. Xiao, V. S. Batista and B. Strodel.
Biophys. J., 105, 2323-2332 (2013) [link]

Stability of transmembrane amyloid β-peptide and membrane integrity tested by molecular modeling of site-specific Aβ42 mutations
C. Poojari and B. Strodel.
PLoS ONE, 8: e78399 (2013) [link]

Thermodynamic analysis of structural transitions during GNNQQNY aggregation
K. L. Osborne, M. Bachmann and B. Strodel.
Proteins: Struct. Func. Bioinf., 81:1141–1155 (2013) [link]

Protein structure prediction using global optimization by basin-hopping with NMR shift restraints.
F. Hoffmann and B. Strodel.
J. Chem. Phys., 138:025102 (2013). [link]

How the amyloid-β peptide and membranes affect each other: an extensive simulation study.
C. Poojari, A. Kukol and B. Strodel.
BBA-Biomembranes, 1828, 327-339 (2013).[link]

Molecular modeling, dynamics, and an insight into the structural inhibition of cofactor independent phosphoglycerate mutase isoform 1 from Wuchereria bancrofti using cheminformatics and mutational studies.
O. P. Sharma, Y. Vadlamudi, Q. Liao, B. Strodel, and M. Suresh Kumar.
J. Biomol. Struct. Dyn., 31, 765-778 (2013).[link]

2007-2012

Structures of the Amyloid β-Peptides Aβ_1-40 and Aβ_1-42 as Influenced by pH and a D-Peptide
O.O. Olubiyi and B. Strodel.
J. Phys. Chem. B, 116, 3280-3291 (2012). [link]

Molecular modeling of human alkaline sphingomyelinase
P. S. Suresh, O. Olubiyi, C. Thirunavukkarasu, B. Strodel, M. S. Kumar
Bioinformation, 6, 78-82 (2011).[link]

Modelling Proteins: Conformational Sampling and Reconstruction of Folding Kinetics
K. Klenin, B. Strodel, D.J. Wales and W. Wenzel.
BBA-Proteins and Proteomics, 1814, 977-1000 (2011). [link]

Transmembrane structures for Alzheimer's Aβ_1-42 oligomers.
B. Strodel, J.W.L. Lee, C.S. Whittleston and D.J. Wales.
J. Am. Chem. Soc., 132, 13300-13312 (2010). [link]

Interpolation Schemes for Peptide Rearrangements.
M.S. Bauer, B. Strodel, S.N. Fejer, E.F. Koslover and D.J. Wales.
J. Chem. Phys., 132, 054101 (2010). [link]

Symmetrisation of the AMBER and CHARMM Force Fields.
E. Malolepsza, B. Strodel, M. Khalili, S. Trygubenko, S. Fejer and D.J. Wales.
J. Comp. Chem., 31, 1402-1409 (2010). [link]

Frontiers Article: Free Energy Surfaces from an Extended Harmonic Superposition Approach and Kinetics for Alanine Dipeptide.
B. Strodel and D.J. Wales.
Chem. Phys. Lett., 466, 105-115 (2008). [link]

Characterising the first steps of amyloid formation for the ccβ peptide.
B. Strodel, A.W. Fitzpatrick, M. Vendruscolo, C.M. Dobson, and D.J. Wales.
J. Phys. Chem. B 112:9998-10004 (2008). [link]

Implicit solvent models and the energy landscape for aggregation of the amyloidogenic KFFE peptide.
B. Strodel and D.J. Wales.
J. Chem. Theo. Comp. 4:657-672 (2008). [link]

Thermodynamics and Kinetics of Aggregation for the GNNQQNY Peptide.
B. Strodel, C.S. Whittleston, and D.J. Wales.
J. Am. Chem. Soc. 129:16005-16014 (2007). [link]

2003-2006

Classical calculation of transient absorption spectra monitoring ultrafast electron transfer processes.
I. Uspenskiy, B. Strodel, and G. Stock.
J. Chem. Theo. Comp. 2:1605-1617 (2006). [link]

Classical description of the dynamics and time-resolved spectroscopy of nonadiabatic cis-trans photoisomerizations.
I. Uspenskiy, B. Strodel, and G. Stock.
Chem. Phys. 329:109-117 (2006). [link]

Quantum modeling of transient infrared spectra reflecting photoinduced electron-transfer dynamics.
B. Strodel and G. Stock.
J. Chem. Phys. 124:114105 (2006). [link]

Modeling of decoherence and dissipation in nonadiabatic photoreactions by an effective-scaling nonsecular Redfield algorithm.
B. Balzer and G. Stock.
Chem. Phys. 310:33-41 (2005). [link]

Transient spectral features of a cis-trans photoreaction in the condensed phase: A model study.
B. Balzer and G. Stock.
J. Phys. Chem. A 108:6464-6473 (2004). [link]

Mechanism of a photochemical funnel: a dissipative wave-packet dynamics study.
B. Balzer, S. Hahn, and G. Stock.
Chem. Phys. Lett. 379:351-358 (2003). [link]

Quasiclassical and semiclassical wave-packet dynamics n periodic potentials.
B. Balzer, S. Dilthey, G. Stock, and M. Thoss.
J. Chem. Phys. 119:5795-5804 (2003). [link]

Quasiperiodic orbit analysis of nonadiabatic cis-trans photoisomerization dynamics.
B. Balzer, S. Dilthey, S. Hahn, M. Thoss, and G. Stock.
J. Chem. Phys. 119:4204-4215, (2003). [link]

Book Chapters and Proceedings

Molecular simulations of IDPs: From ensemble generation to IDP interactions leading to disorder-to-order transitions
H. Fatafta, S. Samantray, A. Sayyed-Ahmad, O. Coskuner-Weber, B. Strodel
Prog. Mol. Biol. Transl. Sci. 183, 135-185 (2021) [link]
Edited by V. N. Uversky, Elsevier (2021). [link]

Computer simulations of protein-membrane systems. In: Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly
J. Loschwitz, O. O. Olubiyi, J. S. Hub, B. Strodel, C. S.Poojari
Prog. Mol. Biol. Transl. Sci. 170, 273-403 (2020) [link]
Edited by B. Strodel and B. Strodel, Elsevier (2020). [link]

Functional Amyloids.
Carballo-Pacheco M., Barz B. and Strodel B. Proceedings of the 46th IFF Spring School Functional Soft Matter, 23 February - 06 March 2015, Jülich, Germany.

Thermodynamics and kinetics of amyloid aggregation from atomistic simulations.
Barz B. and Strodel B. Proceedings of the Conference Physical Biology of Proteins and Peptides: Theory, Experiment and Simulation, 18 - 20 February 2015, Mexico City, Mexico.

Thermodynamics of Protein Aggregation.
K. L. Osborne, B. Barz, M. Bachmann, and B. Strodel. Phys. Proc., 53, 90-95 (2014) [link]
Proceedings of the 26th Workshop on Recent Developments in Computer Simulation Studies in Condensed Matter Physics, Feb 25-Mar 1, 2013, Athens, Georgia, USA.

Secondary Structure Propensities of the Amyloid β-Peptide Aβ1−42 as Influenced by pH and a D-Peptide.
O. O. Olubiyi, B. Strodel.
In `From Computational Biophysics to Systems Biology (CBSB11)', Proceedings, 20-22 July 2011, Julich, Germany, ISBN 978-3-89336-748-1, pp. 145-150 (2012).

Coarse Grained Simulation of Amyloid Aggregators.
K. Osborne, M. Bachmann, B. Strodel.
In `From Computational Biophysics to Systems Biology (CBSB11)', Proceedings, 20-22 July 2011, Julich, Germany, ISBN 978-3-89336-748-1, pp. 151-155 (2012).

Modeling Transmembrane Amyloid-β Structures: AÎβ-Membrane Interactions.
C. Poojari, B. Strodel.
In `From Computational Biophysics to Systems Biology (CBSB11)', Proceedings, 20-22 July 2011, Julich, Germany, ISBN 978-3-89336-748-1, pp. 157-162 (2012).

Pathways and Rates for Structural Transformations of Peptides and Proteins. In: Energy Flow in Proteins.
D.J. Wales, J.M. Carr, M. Khalili, V. de Souza, B. Strodel, and C.S. Whittleston.
Edited by D.Leitner and J.Straub, Taylor and Francis/CRC Press, 315-340 (2009). [link]