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Items: 1 to 50 of 52

1.

Adaptively Accelerating Reactive Molecular Dynamics Using Boxed Molecular Dynamics in Energy Space.

Shannon RJ, Amabilino S, O'Connor M, Shalishilin DV, Glowacki DR.

J Chem Theory Comput. 2018 Sep 11;14(9):4541-4552. doi: 10.1021/acs.jctc.8b00515. Epub 2018 Aug 21.

PMID:
30044623
2.

Sampling molecular conformations and dynamics in a multiuser virtual reality framework.

O'Connor M, Deeks HM, Dawn E, Metatla O, Roudaut A, Sutton M, Thomas LM, Glowacki BR, Sage R, Tew P, Wonnacott M, Bates P, Mulholland AJ, Glowacki DR.

Sci Adv. 2018 Jun 29;4(6):eaat2731. doi: 10.1126/sciadv.aat2731. eCollection 2018 Jun.

3.

Multiscale analysis of enantioselectivity in enzyme-catalysed 'lethal synthesis' using projector-based embedding.

Zhang X, Bennie SJ, van der Kamp MW, Glowacki DR, Manby FR, Mulholland AJ.

R Soc Open Sci. 2018 Feb 14;5(2):171390. doi: 10.1098/rsos.171390. eCollection 2018 Feb.

4.

A Simple "Boxed Molecular Kinetics" Approach To Accelerate Rare Events in the Stochastic Kinetic Master Equation.

Shannon R, Glowacki DR.

J Phys Chem A. 2018 Feb 15;122(6):1531-1541. doi: 10.1021/acs.jpca.7b12521. Epub 2018 Jan 31.

PMID:
29327936
5.

Characterising the evaporation kinetics of water and semi-volatile organic compounds from viscous multicomponent organic aerosol particles.

Ingram S, Cai C, Song YC, Glowacki DR, Topping DO, O'Meara S, Reid JP.

Phys Chem Chem Phys. 2017 Dec 6;19(47):31634-31646. doi: 10.1039/c7cp05172g.

PMID:
29164191
6.

Pushing the Limits of EOM-CCSD with Projector-Based Embedding for Excitation Energies.

Bennie SJ, Curchod BFE, Manby FR, Glowacki DR.

J Phys Chem Lett. 2017 Nov 16;8(22):5559-5565. doi: 10.1021/acs.jpclett.7b02500. Epub 2017 Nov 2.

PMID:
29076727
7.

Atomistic non-adiabatic dynamics of the LH2 complex with a GPU-accelerated ab initio exciton model.

Sisto A, Stross C, van der Kamp MW, O'Connor M, McIntosh-Smith S, Johnson GT, Hohenstein EG, Manby FR, Glowacki DR, Martinez TJ.

Phys Chem Chem Phys. 2017 Jun 14;19(23):14924-14936. doi: 10.1039/c7cp00492c.

PMID:
28430270
8.

Reaction and relaxation at surface hotspots: using molecular dynamics and the energy-grained master equation to describe diamond etching.

Glowacki DR, Rodgers WJ, Shannon R, Robertson SH, Harvey JN.

Philos Trans A Math Phys Eng Sci. 2017 Apr 28;375(2092). pii: 20160206. doi: 10.1098/rsta.2016.0206.

9.

Fundamentals: general discussion.

Althorpe SC, Beniwal V, Bolhuis PG, Brandão J, Clary DC, Ellis J, Fang W, Glowacki DR, Hele TJ, Jónsson H, Kästner J, Makri N, Manolopoulos DE, McKemmish LK, Menzl G, Miller TF III, Miller WH, Pollak E, Rampino S, Richardson JO, Richter M, Roy Chowdhury P, Shalashilin D, Tennyson J, Welsch R.

Faraday Discuss. 2016 Dec 22;195:139-169. doi: 10.1039/c6fd90077a. No abstract available.

PMID:
27942654
10.

New methods: general discussion.

Angulo G, Astumian RD, Beniwal V, Bolhuis PG, Dellago C, Ellis J, Ensing B, Glowacki DR, Hammes-Schiffer S, Kästner J, Lelièvre T, Makri N, Manolopoulos D, Menzl G, Miller TF, Mulholland A, Oprzeska-Zingrebe EA, Parrinello M, Pollak E, Proppe J, Reiher M, Richardson J, Roy Chowdhury P, Sanz E, Schütte C, Shalashilin D, Szabla R, Taraphder S, Tiwari A, Vanden-Eijnden E, Vijaykumar A, Zinovjev K.

Faraday Discuss. 2016 Dec 22;195:521-556. doi: 10.1039/C6FD90075E. No abstract available.

PMID:
27929586
11.

Application to large systems: general discussion.

Althorpe S, Angulo G, Astumian RD, Beniwal V, Bolhuis PG, Brandão J, Ellis J, Fang W, Glowacki DR, Hammes-Schiffer S, Hele TJ, Jónsson H, Lelièvre T, Makri N, Manolopoulos D, Mebel AM, Menzl G, Miller TF, Parrinello M, Piaggi PM, Pollak E, Roy Chowdhury P, Sanz E, Shalashilin D, Skúlason E, Spezia R, Taraphder S.

Faraday Discuss. 2016 Dec 8. [Epub ahead of print] No abstract available.

PMID:
27929584
12.

Non-adiabatic reactions: general discussion.

Althorpe SC, Ananth N, Angulo G, Astumian RD, Beniwal V, Blumberger J, Bolhuis PG, Ensing B, Glowacki DR, Habershon S, Hammes-Schiffer S, Hele TJ, Makri N, Manolopoulos DE, McKemmish LK, Miller TF III, Miller WH, Mulholland AJ, Nekipelova T, Pollak E, Richardson JO, Richter M, Roy Chowdhury P, Shalashilin D, Szabla R.

Faraday Discuss. 2016 Dec 22;195:311-344. doi: 10.1039/c6fd90078j. No abstract available.

PMID:
27929583
13.

Adaptive free energy sampling in multidimensional collective variable space using boxed molecular dynamics.

O'Connor M, Paci E, McIntosh-Smith S, Glowacki DR.

Faraday Discuss. 2016 Dec 22;195:395-419. doi: 10.1039/c6fd00138f.

14.

Correction to "Toward Nonadiabatic Dynamics of Multichromophore Complexes: A Scalable GPU-Accelerated Exciton Framework.

Sisto A, Glowacki DR, Martinez TJ.

Acc Chem Res. 2016 Jun 21;49(6):1331. doi: 10.1021/acs.accounts.6b00217. Epub 2016 Jun 2. No abstract available.

PMID:
27251301
15.

Non-equilibrium reaction and relaxation dynamics in a strongly interacting explicit solvent: F + CD3CN treated with a parallel multi-state EVB model.

Glowacki DR, Orr-Ewing AJ, Harvey JN.

J Chem Phys. 2015 Jul 28;143(4):044120. doi: 10.1063/1.4926996.

PMID:
26233120
16.

Theoretical chemical kinetics in tropospheric chemistry: methodologies and applications.

Vereecken L, Glowacki DR, Pilling MJ.

Chem Rev. 2015 May 27;115(10):4063-114. doi: 10.1021/cr500488p. Epub 2015 Apr 6. No abstract available.

PMID:
25843545
17.

Reaction dynamics. Vibrational relaxation and microsolvation of DF after F-atom reactions in polar solvents.

Dunning GT, Glowacki DR, Preston TJ, Greaves SJ, Greetham GM, Clark IP, Towrie M, Harvey JN, Orr-Ewing AJ.

Science. 2015 Jan 30;347(6221):530-3. doi: 10.1126/science.aaa0103.

18.

Prediction of enhanced solvent-induced enantioselectivity for a ring opening with a bifurcating reaction path.

Carpenter BK, Harvey JN, Glowacki DR.

Phys Chem Chem Phys. 2015 Apr 7;17(13):8372-81. doi: 10.1039/c4cp05078a. Epub 2014 Dec 18.

PMID:
25521804
19.

A GPU-accelerated immersive audio-visual framework for interaction with molecular dynamics using consumer depth sensors.

Glowacki DR, O'Connor M, Calabró G, Price J, Tew P, Mitchell T, Hyde J, Tew DP, Coughtrie DJ, McIntosh-Smith S.

Faraday Discuss. 2014;169:63-87. doi: 10.1039/c4fd00008k. Epub 2014 Jun 6.

PMID:
25340458
20.

Molecular simulations and visualization: introduction and overview.

Hirst JD, Glowacki DR, Baaden M.

Faraday Discuss. 2014;169:9-22. doi: 10.1039/c4fd90024c. Epub 2014 Oct 6.

PMID:
25285906
21.

Ab initio nonadiabatic dynamics of multichromophore complexes: a scalable graphical-processing-unit-accelerated exciton framework.

Sisto A, Glowacki DR, Martinez TJ.

Acc Chem Res. 2014 Sep 16;47(9):2857-66. doi: 10.1021/ar500229p. Epub 2014 Sep 4. Erratum in: Acc Chem Res. 2016 Jun 21;49(6):1331.

PMID:
25186064
22.

Recent applications of boxed molecular dynamics: a simple multiscale technique for atomistic simulations.

Booth J, Vazquez S, Martinez-Nunez E, Marks A, Rodgers J, Glowacki DR, Shalashilin DV.

Philos Trans A Math Phys Eng Sci. 2014 Aug 6;372(2021). pii: 20130384. doi: 10.1098/rsta.2013.0384.

23.

Unraveling the role of protein dynamics in dihydrofolate reductase catalysis.

Luk LY, Javier Ruiz-Pernía J, Dawson WM, Roca M, Loveridge EJ, Glowacki DR, Harvey JN, Mulholland AJ, Tuñón I, Moliner V, Allemann RK.

Proc Natl Acad Sci U S A. 2013 Oct 8;110(41):16344-9. doi: 10.1073/pnas.1312437110. Epub 2013 Sep 24.

24.

Peptide kinetics from picoseconds to microseconds using boxed molecular dynamics: power law rate coefficients in cyclisation reactions.

Shalashilin DV, Beddard GS, Paci E, Glowacki DR.

J Chem Phys. 2012 Oct 28;137(16):165102. doi: 10.1063/1.4759088.

PMID:
23126740
25.

Interception of excited vibrational quantum states by O2 in atmospheric association reactions.

Glowacki DR, Lockhart J, Blitz MA, Klippenstein SJ, Pilling MJ, Robertson SH, Seakins PW.

Science. 2012 Aug 31;337(6098):1066-9. doi: 10.1126/science.1224106.

26.

MESMER: an open-source master equation solver for multi-energy well reactions.

Glowacki DR, Liang CH, Morley C, Pilling MJ, Robertson SH.

J Phys Chem A. 2012 Sep 27;116(38):9545-60. Epub 2012 Sep 12.

PMID:
22905697
27.

O2(a1Δg) + Mg, Fe, and Ca: experimental kinetics and formulation of a weak collision, multiwell master equation with spin-hopping.

Plane JM, Whalley CL, Frances-Soriano L, Goddard A, Harvey JN, Glowacki DR, Viggiano AA.

J Chem Phys. 2012 Jul 7;137(1):014310. doi: 10.1063/1.4730423.

28.

Protein dynamics and enzyme catalysis: the ghost in the machine?

Glowacki DR, Harvey JN, Mulholland AJ.

Biochem Soc Trans. 2012 Jun 1;40(3):515-21. doi: 10.1042/BST20120047. Review.

PMID:
22616861
29.

Reaction dynamics of CN radicals with tetrahydrofuran in liquid solutions.

Rose RA, Greaves SJ, Abou-Chahine F, Glowacki DR, Oliver TA, Ashfold MN, Clark IP, Greetham GM, Towrie M, Orr-Ewing AJ.

Phys Chem Chem Phys. 2012 Aug 14;14(30):10424-37. doi: 10.1039/c2cp40158d. Epub 2012 Apr 12.

PMID:
22499255
30.

Taking Ockham's razor to enzyme dynamics and catalysis.

Glowacki DR, Harvey JN, Mulholland AJ.

Nat Chem. 2012 Jan 29;4(3):169-76. doi: 10.1038/nchem.1244.

PMID:
22354430
31.

Ultrafast energy flow in the wake of solution-phase bimolecular reactions.

Glowacki DR, Rose RA, Greaves SJ, Orr-Ewing AJ, Harvey JN.

Nat Chem. 2011 Sep 25;3(11):850-5. doi: 10.1038/nchem.1154.

PMID:
22024880
32.

Product energy deposition of CN + alkane H abstraction reactions in gas and solution phases.

Glowacki DR, Orr-Ewing AJ, Harvey JN.

J Chem Phys. 2011 Jun 7;134(21):214508. doi: 10.1063/1.3595259.

PMID:
21663368
33.

Photochemistry: scrambled by the sun?

Ashfold MN, Glowacki DR.

Nat Chem. 2011 Jun;3(6):423-4. doi: 10.1038/nchem.1058. No abstract available.

PMID:
21602851
34.

Chemical Reaction Dynamics in Liquid Solutions.

Orr-Ewing AJ, Glowacki DR, Greaves SJ, Rose RA.

J Phys Chem Lett. 2011 May 19;2(10):1139-44. doi: 10.1021/jz2002716. Epub 2011 Apr 26.

PMID:
26295316
35.

Quasi-classical trajectory study of the dynamics of the Cl + CH4→ HCl + CH3 reaction.

Greaves SJ, Rose RA, Abou-Chahine F, Glowacki DR, Troya D, Orr-Ewing AJ.

Phys Chem Chem Phys. 2011 Jun 21;13(23):11438-45. doi: 10.1039/c0cp02694h. Epub 2011 May 13.

PMID:
21566843
36.

Boxed Molecular Dynamics: Decorrelation Time Scales and the Kinetic Master Equation.

Glowacki DR, Paci E, Shalashilin DV.

J Chem Theory Comput. 2011 May 10;7(5):1244-52. doi: 10.1021/ct200011e. Epub 2011 Apr 19.

PMID:
26610120
37.

Nonstatistical dynamics in unlikely places: [1,5] hydrogen migration in chemically activated cyclopentadiene.

Goldman LM, Glowacki DR, Carpenter BK.

J Am Chem Soc. 2011 Apr 13;133(14):5312-8. doi: 10.1021/ja1095717. Epub 2011 Mar 21.

PMID:
21417477
38.
39.

Vibrationally quantum-state-specific reaction dynamics of H atom abstraction by CN radical in solution.

Greaves SJ, Rose RA, Oliver TA, Glowacki DR, Ashfold MN, Harvey JN, Clark IP, Greetham GM, Parker AW, Towrie M, Orr-Ewing AJ.

Science. 2011 Mar 18;331(6023):1423-6. doi: 10.1126/science.1197796. Epub 2011 Feb 3.

40.

Experimental and modeling studies of the pressure and temperature dependences of the kinetics and the OH yields in the acetyl + O2 reaction.

Carr SA, Glowacki DR, Liang CH, Baeza-Romero MT, Blitz MA, Pilling MJ, Seakins PW.

J Phys Chem A. 2011 Feb 17;115(6):1069-85. doi: 10.1021/jp1099199. Epub 2011 Jan 14.

PMID:
21235214
41.

Alkene hydroboration: hot intermediates that react while they are cooling.

Glowacki DR, Liang CH, Marsden SP, Harvey JN, Pilling MJ.

J Am Chem Soc. 2010 Oct 6;132(39):13621-3. doi: 10.1021/ja105100f.

PMID:
20831167
42.

Unimolecular reactions of peroxy radicals in atmospheric chemistry and combustion.

Glowacki DR, Pilling MJ.

Chemphyschem. 2010 Dec 17;11(18):3836-43. doi: 10.1002/cphc.201000469.

PMID:
20815008
43.

Temperature dependent kinetics (195-798 K) and H atom yields (298-498 K) from reactions of (1)CH(2) with acetylene, ethene, and propene.

Gannon KL, Blitz MA, Liang CH, Pilling MJ, Seakins PW, Glowacki DR.

J Phys Chem A. 2010 Sep 9;114(35):9413-24. doi: 10.1021/jp102276j.

PMID:
20704298
44.

Boxed molecular dynamics: a simple and general technique for accelerating rare event kinetics and mapping free energy in large molecular systems.

Glowacki DR, Paci E, Shalashilin DV.

J Phys Chem B. 2009 Dec 31;113(52):16603-11. doi: 10.1021/jp9074898.

PMID:
19961166
45.

Significance of nonstatistical dynamics in organic reaction mechanisms: time-dependent stereoselectivity in cyclopentyne-alkene cycloadditions.

Glowacki DR, Marsden SP, Pilling MJ.

J Am Chem Soc. 2009 Oct 7;131(39):13896-7. doi: 10.1021/ja9043054.

PMID:
19746970
46.

Comment on "Primary atmospheric oxidation mechanism for toluene".

Jenkin ME, Glowacki DR, Rickard AR, Pilling MJ.

J Phys Chem A. 2009 Jul 16;113(28):8136-8; discussion 8139-40. doi: 10.1021/jp903119k. No abstract available.

PMID:
19537748
47.

Evidence of formation of bicyclic species in the early stages of atmospheric benzene oxidation.

Glowacki DR, Wang L, Pilling MJ.

J Phys Chem A. 2009 May 7;113(18):5385-96. doi: 10.1021/jp9001466.

PMID:
19351166
48.

Classical, quantum and statistical simulations of vibrationally excited HOSO(2): IVR, dissociation, and implications for OH + SO(2) kinetics at high pressures.

Glowacki DR, Reed SK, Pilling MJ, Shalashilin DV, Martínez-Núñez E.

Phys Chem Chem Phys. 2009 Feb 14;11(6):963-74. doi: 10.1039/b816108a. Epub 2008 Dec 11.

PMID:
19177215
49.
50.

A combined experimental and theoretical study of the reaction between methylglyoxal and OH/OD radical: OH regeneration.

Baeza-Romero MT, Glowacki DR, Blitz MA, Heard DE, Pilling MJ, Rickard AR, Seakins PW.

Phys Chem Chem Phys. 2007 Aug 21;9(31):4114-28. Epub 2007 May 22.

PMID:
17687462

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