unizeit | nano sciences | natural sciences & mathematics | technology
unizeit Schriftzug

Algorithmssupplementingthechemistrylab

Somechemicalprocessesaresocomplexthatitisalmostimpossibletosaywhatishappeningexactly.Computer-assistedmethods,asdevelopedbyassistantprofessorCarolinKnig,cansimulatetheseprocessesandtherebyhelpustounderstandthembetter.

Luminous molecules on black background
PeterNilsson

Specialluminousmoleculessettleonabnormalproteinstructuresandcantherebyindicatecertainbraindiseases.TheoreticalchemistCarolinKnigisresearchingtheprocessestakingplacehere.

Proteinscarryoutdifferenttasksinourbodies.Ifmodifiedexternally,theycanbeanindicatorforvariousdiseases.Specialmoleculestargetanddockonthesedefectiveproteinstructuresandactasatypeofwarningsignal.Theseso-calledbiomarkersareusedasindicatorsformedicaldiagnoses.

Wecouldimprovethefunctionofbiomarkersevenfurtherifweunderstoodmoreexactlythemechanismsofthechemicalprocessestakingplacethere,saidCarolinKnig,assistantprofessorattheInstituteofPhysicalChemistry.Sheisprimarilyresearchingbiomarkersforamyloidfibrilsabnormalproteinstructuresinthenervecellsofthebrain,whichoccurinconnectionwithdiseaseslikeAlzheimersorParkinsons.Withoptimisedbiomarkers,evenbetterdistinctionscouldbemadebetweenindividualdiseases.TogetherwiththeSwedishLinkpingUniversityandKTHRoyalInstituteofTechnologyinStockholm,Knigisexaminingbiomarkermoleculesthatsettledonthesedefectiveamyloidfibrilstructures.Throughexperiments,however,itisalmostimpossibletoexaminewhichprocessesaretakingplaceindetail.

Therearesomanyparametersinteractinginthereactionsoccurringaroundthesebiomarkersthatwecannevercalculateallofthem.

CarolinKnig

Knigusesmethodsfromquantummechanicstotrackthemechanismsbehindthebiomarkers.Theideaoftheoreticalchemistry,thatofmathematicallycalculatingandthereforepredictingthebehaviourofmoleculesorindividualatoms,aswellastherequiredbasicequations,hasexistedforquitealongtime.Butisitonlyinthelastfewdecadesthatimprovedalgorithmsandmoreeffectivecomputershaveenabledaccurateresultstobeproducedevenforcomplexsystems.Evenwithmodernmethods,calculationsforthesecantakeseveralweeksonlarge-scalecomputerequipment.

Portrait of Carolin König
JuliaSiekmann

CarolinKnig

Yetinexaminingbiomarkersthatindicatecertainbraindiseases,high-performancecomputersalonearealmostnofurtherhelptoKnig.Therearesomanyparametersinteractinginthereactionsoccurringaroundthesebiomarkersthatwecannevercalculateallofthem,saidKnig,describingabasicproblemoftheoreticalchemistry.Evenwiththeexpectedimprovementincomputerperformance,thecalculationswouldtakemuchtoolong.Thenumberofparametersinvolvedwillatsomepointequalthenumberofstarsintheuniversethatisthemagnitudethatwearedealingwithhere.

Inordertoestablishalgorithmsthatcanberealisticallyexecuted,Knigplanstoconcentrateprimarilyonparametersthathaveadecisiveinfluenceontheresult.Reactionsoftenonlyoccurinasmallpartofaprotein.Knigplanstoexaminetheselocalprocesseswithaccuratebuttime-consumingcalculations,whileapplyingsimplerapproximationsinregionswherenocentralreactionstepstakeplace.Thiscombinationofmethodsgivesusacalculationthatisasaccurateaspossiblebutnottoocomplexandcanthereforestillbeexecuted,explainedthetheoreticalchemist.

Thedevelopmentofsuchmulti-scalemethods,whichcombinevariousapproaches,isanemergingresearchfield.Thereisstillalottodiscoverhereandalotisstillpossible.Ifindthatexciting,saidKnig.TheawardingoftheNobelPrizeforChemistryin2013tothreeUSresearchersworkinginthisfielddemonstratestheimportanceandpotentialofthesubject.

Author:JuliaSiekmann

EmmyNoetherresearchgroup

TheGermanResearchFoundation(DFG)promotesthedevelopmentofnewmethodsincomputerchemistrythroughitsprovisionofanEmmyNoetherresearchgroupandaroundhalfamillioneurosforfiveyears.GroupleaderandassistantprofessorCarolinKnigplanstousethisfundingtoexamine,amongotherthings,specialbiomarkersthatindicatebraindiseaseslikeAlzheimersandParkinsons.TheEmmyNoetherProgrammeenablesoutstandingyoungresearcherstoqualifyearlyforaprofessorshipbyleadingtheirownworkinggroup.(jus)